Rui:Data Analysis

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Revision as of 17:14, 9 August 2011 by >RuiLiu (→‎RNAseq analysis on HL098)
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Examples

Jeff's samples:
Kun:LabNotes/Haplotyping/2010-9-17 [1]
Transcriptome:
Kun:LabNotes/SingleCellExpr/2011-6-13 [2]
Haplotyping:
Kun:LabNotes/Haplotyping/2011-6-14 [3]

Haplotyping 6.21.11

Data

ruiliu@genome-miner:~$ cd /home/kunzhang/haplotyping/Data/HL095/

ruiliu@genome-miner:/home/kunzhang/haplotyping/Data/HL095$ ls -l s_4_Indx1.*

-rw-r--r-- 1 kunzhang kunzhang 114237942 2011-06-13 22:07 s_4_Indx1.bowtie.pileup
-rw-r--r-- 1 kunzhang kunzhang  39977658 2011-06-13 21:28 s_4_Indx1.bowtie.sorted.bam
-rw-r--r-- 1 kunzhang kunzhang   4442210 2011-06-13 22:05 s_4_Indx1.bowtie.sorted.unique.bam
-rw-r--r-- 1 kunzhang kunzhang       278 2011-06-13 21:29 s_4_Indx1.bowtie.variants.txt
-rw-r--r-- 1 kunzhang kunzhang      7103 2011-06-14 15:58 s_4_Indx1.hapCompare.txt
-rw-r--r-- 1 kunzhang kunzhang      9399 2011-06-14 16:56 s_4_Indx1.idioGraph.txt
-rw-r--r-- 1 kunzhang kunzhang    675115 2011-06-13 21:29 s_4_Indx1.log
-rw-r--r-- 1 kunzhang kunzhang 273522562 2011-06-13 18:08 s_4_Indx1.txt

ruiliu@genome-miner:/home/kunzhang/haplotyping/Data/HL095$ less s_4_Indx1.bowtie.pileup

1       557399  C       A       25      25      25      1       ^:A     f
1       557400  A       A       25      0       25      1       .       f
1       557401  T       T       25      0       25      1       .       f
1       557402  C       C       25      0       25      1       .       f
1       557403  A       A       25      0       25      1       .       c
1       557404  C       C       25      0       25      1       .       g
1       557405  T       T       25      0       25      1       .       g
1       557406  A       A       25      0       25      1       .       g
1       557407  G       G       25      0       25      1       .       g
1       557408  A       A       25      0       25      1       .       e
1       557409  C       C       25      0       25      1       .       f

ruiliu@genome-miner:/home/kunzhang/haplotyping/Data/HL095$ more s_4_Indx11.log

/home/kunzhang/softwares/bowtie-latest/bowtie -k 1 -l 32 -n 2 -m 1 --best --quiet -p 4 /home/kunzhang/HsGenome/1KG.ref/HsB36m s_4_Indx
11.txt s_4_Indx11.bowtie.map.1 
/home/kunzhang/Exome/Data/scripts/trimTerminalMismatches.pl < s_4_Indx11.bowtie.map.1 > s_4_Indx11.bowtie.map.2
/home/kunzhang/softwares/samtools-0.1.7_x86_64-linux/bowtie2sam.pl  s_4_Indx11.bowtie.map.2 > s_4_Indx11.bowtie.sam
/home/kunzhang/softwares/samtools-0.1.7_x86_64-linux/samtools import /home/kunzhang/HsGenome/1KG.ref/human_b36_male.fa.gz.fai s_4_Indx
11.bowtie.sam s_4_Indx11.bowtie.bam
[sam_header_read2] 114 sequences loaded.
/home/kunzhang/softwares/samtools-0.1.7_x86_64-linux/samtools sort s_4_Indx11.bowtie.bam  s_4_Indx11.bowtie.sorted
java -Xmx2g -jar /home/kunzhang/softwares/picard-tools-1.38/MarkDuplicates.jar ASSUME_SORTED=TRUE REMOVE_DUPLICATES=TRUE INPUT=s_4_In
dx11.bowtie.sorted.bam OUTPUT=s_4_Indx11.bowtie.sorted.unique.bam METRICS_FILE=dup.metric
[Tue Jun 14 15:23:03 PDT 2011] net.sf.picard.sam.MarkDuplicates INPUT=s_4_Indx11.bowtie.sorted.bam OUTPUT=s_4_Indx11.bowtie.sorted.uni
que.bam METRICS_FILE=dup.metric REMOVE_DUPLICATES=true ASSUME_SORTED=true    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDL
ES_FOR_READ_ENDS_MAP=8000 READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).* OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 TMP_DIR
=/tmp/kunzhang VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=fals
e CREATE_MD5_FILE=false
INFO	2011-06-14 15:23:03	MarkDuplicates	Start of doWork freeMemory: 374846832; totalMemory: 377225216; maxMemory: 1908932608
INFO	2011-06-14 15:23:03	MarkDuplicates	Reading input file and constructing read end information.
INFO	2011-06-14 15:23:03	MarkDuplicates	Will retain up to 7575129 data points before spilling to disk.
INFO	2011-06-14 15:23:03	MarkDuplicates	Assuming input is coordinate sorted.
INFO	2011-06-14 15:23:06	MarkDuplicates	Read 887559 records. 0 pairs never matched.
INFO	2011-06-14 15:23:07	MarkDuplicates	After buildSortedReadEndLists freeMemory: 733397640; totalMemory: 925368320; maxMemory
: 1908932608
INFO	2011-06-14 15:23:07	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
INFO	2011-06-14 15:23:07	MarkDuplicates	Traversing read pair information and detecting duplicates.
INFO	2011-06-14 15:23:07	MarkDuplicates	Traversing fragment information and detecting duplicates.
INFO	2011-06-14 15:23:09	MarkDuplicates	Sorting list of duplicate records.
INFO	2011-06-14 15:23:09	MarkDuplicates	After generateDuplicateIndexes freeMemory: 923987040; totalMemory: 1410072576; maxMemo
ry: 1908932608
INFO	2011-06-14 15:23:09	MarkDuplicates	Marking 837865 records as duplicates.
INFO	2011-06-14 15:23:09	MarkDuplicates	Found 0 optical duplicate clusters.
INFO	2011-06-14 15:23:12	MarkDuplicates	Before output close freeMemory: 920285040; totalMemory: 1408237568; maxMemory: 1908932
608
INFO	2011-06-14 15:23:12	MarkDuplicates	After output close freeMemory: 876964080; totalMemory: 1364918272; maxMemory: 19089326
08
[Tue Jun 14 15:23:12 PDT 2011] net.sf.picard.sam.MarkDuplicates done.
Runtime.totalMemory()=1364918272
/home/kunzhang/softwares/samtools-0.1.7_x86_64-linux/samtools pileup -c -f /home/kunzhang/HsGenome/1KG.ref/human_b36_male.fa s_4_Indx1
1.bowtie.sorted.unique.bam > s_4_Indx11.bowtie.pileup
Use of uninitialized value in print at /home/kunzhang/Exome/Data/scripts/pileup2variants.pl line 145.
Use of uninitialized value in print at /home/kunzhang/Exome/Data/scripts/pileup2variants.pl line 145.

ruiliu@genome-miner:/home/kunzhang/haplotyping/Data/HL095$ /home/kunzhang/softwares/samtools-0.1.7_x86_64-linux/samtools view s_4_Indx11.bowtie.sorted.bam | wc -l

887559

ruiliu@genome-miner:/home/kunzhang/haplotyping/Data/HL095$ /home/kunzhang/softwares/samtools-0.1.7_x86_64-linux/samtools view s_4_Indx11.bowtie.sorted.unique.bam | wc -l

49694

Reads

Barcode Reads Unique Percentage
Indx1 163556 15899 9.7
Indx2 196625 16718 8.5
Indx3 127140 10123 8.0
Indx4 189464 13511 7.1
Indx5 9536 4856 50.9
Indx6 220670 12779 5.8
Indx7 185404 12479 6.7
Indx8 209445 14185 6.8
Indx9 175999 12100 6.9
Indx10 212683 13919 6.5
Indx11 188707 14591 7.7
Indx12 326082 16300 5.0


RNAseq analysis from 7.18.11

  1. ID1 and ID2 are human samples; ID3-6 are mouse samples. De-multiplexing will give clearer idea on library mapping.
  2. Combine them into a single file, I can first check the sequencing quality with Galaxy.
  3. Athurva converted qseq files (55bp) for lane 1 (120) into a single fastq file [ruiliu@genome-miner:~/RNAseq/s_1_1_sequence.txt]
  4. s_1_1_sequence.txt: 4.4 GB, 50 million lines [wc -l s_1_1_sequence.txt]
  5. [head -n 1000000 s_1_1_sequence.txt] for the firstmillion lines [ruiliu@genome-miner:~/RNAseq/firstmillion.txt] uploaded to Galaxy (up limit is 2GB)
  6. Groomer --> fastq summary statistics (250000 fastq reads) --> compute quality statistics (good) --> draw quality score boxplot (40-35) --> Tophat (accepted hits /splice junction) --> flagstat (143296 in total, 0 QC failure, 0 duplicates, 143296 mapped (100.00%), 0 paired in sequencing, 0 read1) --> Mark Duplicate reads (empty??)
  7. To upload the original file (4GB), zip it to [tar -zcvf ~/new.tar.gz s_1_sequence.txt] new.tar.gz under home directly (permission issue), download to my laptop and install Cyberduck on Mac to upload file via FTP [main.g2.bx.psu.edu] with username [bsos@ucsd.edu] and password [zhanglab]

overview of reads

Questions:

  1. Which one is the mappable reads?
  2. Clonal reads can't be removed if the expression level is compared, right? So stopping PCR at exponential stage is critical. Low expressed RNAs will be sacrificed to high expressed RNAs if over-amplifying RNAs and total input amount is limited for sequencing. And eventually, increasing clonal reads will decrease sequencing coverage, right? But still, PCR amplification plus clustering could also lead inaccuracy in expression level estimate, right?
  3. Percentage of reads after clonal reads removal to mappable reads in Ind1 to Ind4 is similar (76%; 76.7%; 76.8%;78%), which means these libraries are almost evenly amplified, right?.
  4. Multiple loci reads also can't be removed b/c short reads of coding sequence are possibly mapped to paralogs, right?
110714_HL098 ' ' FASTQ stat. ' ' TopHat ' ' removeClonalHits.pl ' ' ' ' '
ID Sample file size fastq reads ASCII range Decimal range Genome Accepted hits Junction mapped reads % of total pro-rm clonal reads % of total then uniquely mapped % of total
s_1_Indx1 GFP+ 531.5MB 2,307,029 #\'(35) - \'I\'(73) 2-40 Hs 19 889,766 36,435 718,472 0.3114 546,308 0.236801531 511,691 0.221796518
s_1_Indx2 GFP- 709.3MB 3,078,335 \'B\'(66) - \'h\'(104) 33-71 Hs 19 1,963,553 61,496 1,615,433 0.5248 1,237,498 0.402002381 1,170,098 0.380107428
s_1_Indx3 E9.5 563.4MB 2,445,243 \'B\'(66) - \'h\'(104) 33-71 mm 9 1,983,651 47,929 1,491,621 0.6100 1,143,810 0.467769461 1,039,861 0.425258758
s_1_Indx4 E11.5 886.9MB 3,849,227 \'B\'(66) - \'h\'(104) 33-71 mm 9 1,618,640 44,625 1,208,317 0.3139 951,936 0.247305758 856,563 0.222528575


Run Tophat in meangenemachine

Bowtie Index

  • Download Hs19
 Wget ftp://ftp.ncbi.nih.gov/genomes/H_Sapine/Assambled_chromosome/hs_ref_GRCh37.p2*.fa.gz
  • Combine all together
 less *.gz > hs_ref_GRCh37.fa
  • Bowtie Index
 bowtie-build hs_ref_GRCh37.fa hs_ref_GRCh37 > log.blablabla

Sequence files

  • check fastq file with ASCII table to see if 33 code or 64 code
  • combine 2 ends files into 1 file (somehow, less command is not working well in Mac)
 cat file1.gz file2.gz | gunzip > new file
  • substitute "#0/3" with "#03" (reason: position confusion in the sorted.acceptedhit.sam file generated from TopHat,esp. running removalclonalread.ps after that; more information for sed : http://www.grymoire.com/Unix/Sed.html#uh-0)
 sed 's:#0/3:#03:g' file > newfile
 sed 's/#0\/3/#03/g' file > newfile
  • run QC for each file and download
 ~/RNAseqTools/fastqc file
  • run Tophat
 in /BowtieIndices/ to find the human or mm ref
 tophat -p 4 --solexa1.3-quals /media/1TB_store1/BowtieIndices/mm_ref_MGSCv37 file &
 For pair-end:
 tophat -p 4 --solexa1.3-quals -r "distance" --mate-std-dev "STDEV" -o "output" /media/1TB_store1/BowtieIndices/hs_ref_GRCh37.p2 file &

Tophat summary

110714_HL098 ' ' TopHat ' ' ' ' ' removeClonalHits.pl ' ' ' ' ' '
ID Sample file size fastq reads in reads out Genome Accepted hits Junction mapped reads % of total pro-rm clonal reads % of total % of mappable reads then uniquely mapped % of total
s_1_Indx1 GFP+ 1,063,078,988 4,614,058 4,605,533 0.9982 Hs 19 1,819,753 1,646,034 0.3567 1,191,550 0.2582 0.723891487 1,140,325 0.2471
s_1_Indx2 GFP- 1,418,503,096 6,156,670 6,145,196 0.9981 Hs 19 4,156,441 3,742,990 0.6080 2,637,547 0.428404803 0.704663117 2,543,973 0.413206003
s_1_Indx3 E9.5 1,126,757,636 4,890,486 4,881,588 0.9982 mm 9 4,483,009 3,529,559 0.7217 2,350,598 0.480647118 0.665974984 2,192,476 0.448314544
s_1_Indx4 E11.5 1,773,739,660 7,698,454 7,685,366 0.9983 mm 9 3,537,587 2,757,814 0.3582 1,915,170 0.248773325 0.6944522 1,771,219 0.230074636
s_1_Indx5 E13.5m 4,002,812,404 17,373,520 17,342,655 0.9982 mm 9 6,601,730 5,227,070 0.3009 3,214,319 0.1850 0.614937049 3,023,072 0.1740
s_1_Indx6 E13.5f 4,927,760,680 21,387,852 21,349,698 0.9982 mm 9 5,999,758 4,744,699 0.221840837 2,967,058 0.13872632 0.625341671 2,783,215 0.130130646


Cell numbers

ID Sample RNA amount Cell numbers % of mappable read to total
s_1_Indx1 GFP+ 20ng 0.2471
s_1_Indx2 GFP- 12ng 0.413206003
s_1_Indx3 E9.5 ~316 cells 0.448314544
s_1_Indx4 E11.5 ~2000 cells 0.230074636
s_1_Indx5 E13.5m ~3000 cells 0.1740
s_1_Indx6 E13.5f ~3000 cells 0.130130646

Flowchart

File:Flowchart 1.jpg

File:Flowchart 2.jpg

Summary on Tophat/cufflinks/cuffcompare/cuffdiff

Tophat

  • reads results from single end mapping and from paired end mapping are quite similar; parameters such as internal-length and STDEV have least, if not no, effect.
  • Paired end mapping provide more accurate information, and show significant difference when using cufflinks
' ' ' TopHat ' ' ' ' ' ' ' ' removeClonalHits.pl ' ' ' ' ' ' '
Sample file size fastq reads in reads out Genome Accepted hits hits from each read mapped pairs (up) mapped single (down) properly located pairs % of total mapped reads % of total pro-rm clonal reads % of total % of mappable reads then uniquely mapped % of total potential coverage
s_1_Indx1 GFP+ 1,063,078,988 4,614,058 4,605,533 0.9982 Hs 19 1,819,753 1,646,034 0.3567 1,191,550 0.2582 0.7239 1,140,325 0.2471 0.045613
s_1_Indx2 GFP- 1,418,503,096 6,156,670 6,145,196 0.9981 Hs 19 4,156,441 3,742,990 0.6080 2,637,547 0.4284 0.7047 2,543,973 0.4132 0.10175892
s_1_Indx1 s_1_1_Indx1 left read 2,307,029 2,300,738 0.9973 r:225 1,706,112 734,674 1,122,672 0.658029485 1,615,377 0.3501 1,191,056 0.2581 0.7373 1,160,088 0.2514 0.04640352
s_1_2_Indx1 right read 2,307,029 2,304,795 0.9990 STD:212 971,438 583,440 955,602 0.560105081
s_1_Indx2 s_1_1_Indx2 left read 3,078,335 3,069,878 0.9973 3,881,050 1,679,506 2,749,076 0.708333054 3,678,975 0.5976 2,642,078 0.4291 0.7182 2,585,404 0.4199 0.10341616
s_1_2_Indx2 right read 3,078,335 3,075,318 0.9990 2,201,544 1,131,974 2,346,216 0.604531248
s_1_Indx1 s_1_1_Indx1 left read 2,307,029 2,300,738 0.9973 r:250 1,705,993 734,602 1,122,540 0.657998011 1,615,384 0.3501 1,191,029 0.2581 0.7373 1,160,079 0.2514 0.04640316
s_1_2_Indx1 right read 2,307,029 2,304,795 0.9990 STD:80 971,391 583,453 941,458 0.551853378
s_1_Indx2 s_1_1_Indx2 left read 3,078,335 3,069,878 0.9973 3,882,019 1,679,990 2,750,090 0.70841745 3,678,987 0.5976 2,642,026 0.4291 0.7181 2,585,255 0.4199 0.1034102
s_1_2_Indx2 right read 3,078,335 3,075,318 0.9990 2,202,029 1,131,929 2,293,768 0.590869854

Cufflinks

  • cufflinks: processing loci greatly differ in SE/PE mapping and correction with GTF (tip: RefFlast from Refseq in UCSC, can't used gene_id from Ensemble, if gene name is expected in output files)
  • Correction wit GTF largely reduced loci input and # of output in genes/isoforms (cufflinks, cuffcompare and cuffdiff), probably due to better annotation? (guess, can't find details in manual or paper...)
  • No much parameter options for cuffcompare or cuffdiff
  • Odd: different gene_exp in tophat_225_212 and tophat_250_80 are exactly same, although they are different in any other results.
' ' cufflinks ' ' ' cuffcompare ' ' ' ' ' cuffdiff '
loci total map mass wc -l Missed exons Wrong exons Missed introns Wrong introns Missed loci Wrong loci gene isoform
tophat_SE Indx1 131,431 1645874.66 66,396 42.60% 7.40% 48.50% 0.30% 0.00% 23.40% 1745 4623
Indx2 203,286 3742794.31 117,273 37.90% 8.50% 42.80% 0.60% 0.00% 27.10%
tophat_PE Indx1_left 95,470 1076008.63 29,623 43.20% 5.60% 48.40% 0.20% 0.00% 19.90% 332* 646
225/212 Indx1_right (-g) 40,331 441,677
Indx2_left 39.50% 5.30% 43.80% 0.20% 0.00% 19.90%
Indx2_right
tophat_PE Indx1_left
250/80 Indx1_right (-g) 40,341 1076014.17 441,831 0.00% 0.30% 0.20% 0.00% 0.00% 2.50% 332* 1462
Indx2_left
Indx2_right (-g) 63,059 2361671.63 459,770 0.00% 0.60% 0.20% 0.10% 0.00% 4.10%


RNAseq analysis on HL098

Database download

iGenome collection [4], save in ~/iGenome/

  • BowtieIndex: ~/iGenome/Homo_sapiens/UCSC/hg19/Sequence/BowtieIndex | ~/iGenome/Mus_musculus/UCSC/mm9/Sequence/BowtieIndex
  • Annotation: ~/iGenome/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.gtf

Tophat

nohup tophat -p 6 --solexa1.3-quals -o ./tophat-g/ -r 250 --mate-std-dev 80 -G ~/iGenome/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.gtf ~/iGenome/Homo_sapiens/UCSC/hg19/Sequence/BowtieIndex/genome ./seq/s_1_1_Indx1.txt ./seq/s_1_2_Indx1.mod.txt

nohup tophat -p 6 --solexa1.3-quals -o ./tophat-g/ -r 250 --mate-std-dev 80 -G ~/iGenome/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.gtf ~/iGenome/Homo_sapiens/UCSC/hg19/Sequence/BowtieIndex/genome ./seq/s_1_1_Indx2.txt ./seq/s_1_2_Indx2.mod.txt

Samtools and clonalreads removal

samtools flagstat accepted_hits.bam

~/RNAtools/removalclonalreads.pl accepted_hits.bam


Pair-end mapping ' ' ' ' ' Tophat ' ' ' ' ' removeClonalHits.pl ' ' ' ' ' ' '
file size fastq reads in reads out % options accepted hits reads hits pair/single Properly paired % of total mapped reads % of total pro-rm clonal reads % of total % of mappable reads then uniquely mapped % of total potential coverage
s_1_Indx1 s_1_1_Indx1 left read 2,307,029 2,300,738 0.9973 r:250 1,705,993 734,602 1,122,540 0.657998011 1,615,384 0.3501 1,191,029 0.2581 0.7373 1,160,079 0.2514 0.04640316
s_1_2_Indx1 right read 2,307,029 2,304,795 0.9990 STD:80 971,391 583,453 941,458 0.551853378
s_1_Indx1 s_1_1_Indx1 left read 2,307,029 2,300,738 0.9973 (+g) 1,733,904 746,989 1,156,628 0.667065766 1,643,007 0.3561 1,218,033 0.2640 0.7413 1,186,899 0.2572 0.04747596
s_1_2_Indx1 right read 2,307,029 2,304,795 0.9990 UCSC 986,915 577,276 965,638 0.556915492
s_1_Indx2 s_1_1_Indx2 left read 3,078,335 3,069,878 0.9973 r:250 3,882,019 1,679,990 2,750,090 0.70841745 3,678,987 0.5976 2,642,026 0.4291 0.7181 2,585,255 0.4199 0.1034102
s_1_2_Indx2 right read 3,078,335 3,075,318 0.9990 STD:80 2,202,029 1,131,929 2,293,768 0.590869854
s_1_Indx2 s_1_1_Indx2 left read 3,078,335 3,069,878 0.9973 (+g) 3,913,815 1,694,018 2,792,224 0.713427691 3,711,732 0.6029 2,674,065 0.4343 0.7204 2,617,136 0.4251 0.10468544
s_1_2_Indx2 right read 3,078,335 3,075,318 0.9990 UCSC 2,219,797 1,121,591 2,344,834 0.59911723

Cufflinks and cuffdiff

samtools view -h ../accepted_hits.bam > accepted_hits.sam (have to convert to sam first, i can't feed cufflinks with bam file --- error: segment fault...)

cufflinks -g ~/iGenome/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.gtf -m 250 -s 80 accepted_hits.sam (-g option is probably unnecessary...)


RNAseq analysis on HL099

=Download files from SeqStore

ID Sample file size relative ratio
HL098 s_1_Indx1.txt 1,063,078,988 0.75
HL098 s_1_Indx2.txt 1,418,503,096 1.00
HL098 s_1_Indx3.txt 1,126,757,636 0.79
HL098 s_1_Indx4.txt 1,773,739,660 1.25
HL098 s_1_Indx5.txt 4,002,812,404 2.82
HL098 s_1_Indx6.txt 4,927,760,680 3.47
10.09
HL099 s_2_Indx1.txt 799,803,430 0.73
HL099 s_2_Indx2.txt 1,088,795,544 1.00
HL099 s_2_Indx3.txt 816,515,216 0.75
HL099 s_2_Indx4.txt 668,702,922 0.61
HL099 s_2_Indx5.txt 1,263,996,032 1.16
HL099 s_2_Indx6.txt 1,152,064,234 1.06
5.32
HL099 s_3_Indx1.txt 2,055,529,230 1.58
HL099 s_3_Indx2.txt 1,300,750,376 1.00
HL099 s_3_Indx3.txt 1,054,455,616 0.81
HL099 s_3_Indx4.txt 1,205,324,668 0.93
HL099 s_4_Indx1.txt 2,075,122,264 1.59
HL099 s_4_Indx2.txt 1,308,387,872 1.00
HL099 s_4_Indx3.txt 1,057,664,912 0.81
HL099 s_4_Indx4.txt 1,212,653,382 0.93
HL099 s_5_Indx1.txt 1,942,428,848 1.58
HL099 s_5_Indx2.txt 1,225,815,974 1.00
HL099 s_5_Indx3.txt 984,527,600 0.80
HL099 s_5_Indx4.txt 1,129,401,814 0.92
HL099 s_6_Indx1.txt 2,046,395,112 1.58
HL099 s_6_Indx2.txt 1,292,688,682 1.00
HL099 s_6_Indx3.txt 1,044,933,252 0.81
HL099 s_6_Indx4.txt 1,189,162,084 0.92
' ' ' ' ' ' Tophat removeClonalHits.pl ' ' ' ' ' ' '
reads in reads out % accepted hits mapped reads % of total pro-rm clonal reads % of total % of mappable reads then uniquely mapped % of total potential coverage
HL099 Indx1 8,919,278,884 46,366,051 46,356,341 0.9998 23,635,554 20,388,632 0.44 8,637,058 0.19 0.42 8,355,371 0.18 0.33421484
HL099 Indx2 6,216,438,448 32,314,674 32,306,989 0.9998 27,114,017 23,424,639 0.72 10,904,543 0.34 0.47 10,567,772 0.33 0.42271088