Editing
Matt:LabNotes/2014-10-31
(section)
Jump to navigation
Jump to search
Warning:
You are not logged in. Your IP address will be publicly visible if you make any edits. If you
log in
or
create an account
, your edits will be attributed to your username, along with other benefits.
Anti-spam check. Do
not
fill this in!
===Align with Tophat2 to hg19=== ~/scratch/RTprimer_Analysis$ /home/kunzhang/softwares/tophat-2.0.6.Linux_x86_64/tophat2 -o tophat_hg19unmask_Indx26_RanHex --solexa1.3-quals ~/LTS/Genomes/hg19 s_8_1_Indx26.txt ~/scratch/RTprimer_Analysis$ /home/kunzhang/softwares/tophat-2.0.6.Linux_x86_64/tophat2 -o tophat_hg19unmask_Indx27_dT --solexa1.3-quals ~/LTS/Genomes/hg19 s_8_1_Indx27.txt ~/scratch/RTprimer_Analysis$ /home/kunzhang/softwares/tophat-2.0.6.Linux_x86_64/tophat2 -o tophat_hg19unmask_Indx28_FISSEQRT --solexa1.3-quals ~/LTS/Genomes/hg19 s_8_1_Indx28.txt ~/scratch/RTprimer_Analysis$ /home/kunzhang/softwares/tophat-2.0.6.Linux_x86_64/tophat2 -o tophat_hg19unmask_Indx29_Top48 --solexa1.3-quals ~/LTS/Genomes/hg19 s_8_1_Indx29.txt *RanHex 586553 reads; of these: 586553 (100.00%) were unpaired; of these: 251516 (42.88%) aligned 0 times 196622 (33.52%) aligned exactly 1 time 138415 (23.60%) aligned >1 times 57.12% overall alignment rate *dT 432896 reads; of these: 432896 (100.00%) were unpaired; of these: 103736 (23.96%) aligned 0 times 215595 (49.80%) aligned exactly 1 time 113565 (26.23%) aligned >1 times 76.04% overall alignment rate *FISSEQRT 529281 reads; of these: 529281 (100.00%) were unpaired; of these: 199427 (37.68%) aligned 0 times 205336 (38.80%) aligned exactly 1 time 124518 (23.53%) aligned >1 times 62.32% overall alignment rate *Top48 523107 reads; of these: 523107 (100.00%) were unpaired; of these: 165872 (31.71%) aligned 0 times 229706 (43.91%) aligned exactly 1 time 127529 (24.38%) aligned >1 times 68.29% overall alignment rate ====Samtools Sort and Index==== samtools sort tophat_hg19unmask_Indx26_RanHex/accepted_hits.bam mapped_RanHex.sorted samtools sort tophat_hg19unmask_Indx27_dT/accepted_hits.bam mapped_dT.sorted samtools sort tophat_hg19unmask_Indx28_FISSEQRT/accepted_hits.bam mapped_FISSEQRT.sorted samtools sort tophat_hg19unmask_Indx29_Top48/accepted_hits.bam mapped_Top48.sorted samtools index mapped_RanHex.sorted.bam mapped_RanHex.sorted.bam.bai samtools index mapped_dT.sorted.bam mapped_dT.sorted.bam.bai samtools index mapped_FISSEQRT.sorted.bam mapped_FISSEQRT.sorted.bam.bai samtools index mapped_Top48.sorted.bam mapped_Top48.sorted.bam.bai fetchChromSizes hg19 > ~/Genomes/hg19.chrom.sizes ====Visual QC==== bam2wig.py -i mapped_RanHex.sorted.bam -s /home/mzcai/LTS/Genomes/hg19.chrom.sizes -o mapped_RanHex.sorted bam2wig.py -i mapped_dT.sorted.bam -s /home/mzcai/LTS/Genomes/hg19.chrom.sizes -o mapped_dT.sorted bam2wig.py -i mapped_FISSEQRT.sorted.bam -s /home/mzcai/LTS/Genomes/hg19.chrom.sizes -o mapped_FISSEQRT.sorted bam2wig.py -i mapped_Top48.sorted.bam -s /home/mzcai/LTS/Genomes/hg19.chrom.sizes -o mapped_Top48.sorted <!-- wigToBigWig wigVarStepExample.gz hg19.chrom.sizes myBigWig.bw --> ====Calculate rRNA Overlap==== =====hg19_rRNA.bed from UCSC table browser===== split_bam.py -i mapped_RanHex.sorted.bam -r /home/mzcai/LTS/Genomes/hg19_rRNA.bed -o split_hg19rRNAbed_RanHex Total records: 398868 split_hg19rRNAbed_RanHex.in.bam (Reads consumed by input gene list):251593 split_hg19rRNAbed_RanHex.ex.bam (Reads not consumed by input gene list):147275 split_hg19rRNAbed_RanHex.junk.bam (qcfailed, unmapped reads):0 split_bam.py -i mapped_dT.sorted.bam -r /home/mzcai/LTS/Genomes/hg19_rRNA.bed -o split_hg19rRNAbed_dT Total records: 422589 split_hg19rRNAbed_dT.in.bam (Reads consumed by input gene list):155754 split_hg19rRNAbed_dT.ex.bam (Reads not consumed by input gene list):266835 split_hg19rRNAbed_dT.junk.bam (qcfailed, unmapped reads):0 split_bam.py -i mapped_FISSEQRT.sorted.bam -r /home/mzcai/LTS/Genomes/hg19_rRNA.bed -o split_hg19rRNAbed_FISSEQRT Total records: 391847 split_hg19rRNAbed_FISSEQRT.in.bam (Reads consumed by input gene list):220685 split_hg19rRNAbed_FISSEQRT.ex.bam (Reads not consumed by input gene list):171162 split_hg19rRNAbed_FISSEQRT.junk.bam (qcfailed, unmapped reads):0 split_bam.py -i mapped_Top48.sorted.bam -r /home/mzcai/LTS/Genomes/hg19_rRNA.bed -o split_hg19rRNAbed_Top48 Total records: 422471 split_hg19rRNAbed_Top48.in.bam (Reads consumed by input gene list):237568 split_hg19rRNAbed_Top48.ex.bam (Reads not consumed by input gene list):184903 split_hg19rRNAbed_Top48.junk.bam (qcfailed, unmapped reads):0 =====Homo_sapiens.GRCh37.75.totalrRNA.chr.bed===== *Bed file from [[Matt:LabNotes/2014-7-14#Bedtools_intersect | gene annotations of Hg19 from Ensembl]] **Converted gtf to bed **[[Matt:LabNotes/2014-7-24#Bedtools_intersect_troubleshooting | Added 'chr' to chromosome names]] split_bam.py -i mapped_RanHex.sorted.bam -r /home/mzcai/LTS/Genomes/Homo_sapiens.GRCh37.75.totalrRNA.chr.bed -o split_GRCh37totalrRNAchrbed_RanHex Total records: 398868 split_GRCh37totalrRNAchrbed_RanHex.in.bam (Reads consumed by input gene list):47 split_GRCh37totalrRNAchrbed_RanHex.ex.bam (Reads not consumed by input gene list):398821 split_GRCh37totalrRNAchrbed_RanHex.junk.bam (qcfailed, unmapped reads):0 split_bam.py -i mapped_dT.sorted.bam -r /home/mzcai/LTS/Genomes/Homo_sapiens.GRCh37.75.totalrRNA.chr.bed -o split_GRCh37totalrRNAchrbed_dT Total records: 422589 split_GRCh37totalrRNAchrbed_dT.in.bam (Reads consumed by input gene list):13 split_GRCh37totalrRNAchrbed_dT.ex.bam (Reads not consumed by input gene list):422576 split_GRCh37totalrRNAchrbed_dT.junk.bam (qcfailed, unmapped reads):0 split_bam.py -i mapped_FISSEQRT.sorted.bam -r /home/mzcai/LTS/Genomes/Homo_sapiens.GRCh37.75.totalrRNA.chr.bed -o split_GRCh37totalrRNAchrbed_FISSEQRT Total records: 391847 split_GRCh37totalrRNAchrbed_FISSEQRT.in.bam (Reads consumed by input gene list):43 split_GRCh37totalrRNAchrbed_FISSEQRT.ex.bam (Reads not consumed by input gene list):391804 split_GRCh37totalrRNAchrbed_FISSEQRT.junk.bam (qcfailed, unmapped reads):0 split_bam.py -i mapped_Top48.sorted.bam -r /home/mzcai/LTS/Genomes/Homo_sapiens.GRCh37.75.totalrRNA.chr.bed -o split_GRCh37totalrRNAchrbed_Top48 Total records: 422471 split_GRCh37totalrRNAchrbed_Top48.in.bam (Reads consumed by input gene list):16 split_GRCh37totalrRNAchrbed_Top48.ex.bam (Reads not consumed by input gene list):422455 split_GRCh37totalrRNAchrbed_Top48.junk.bam (qcfailed, unmapped reads):0
Summary:
Please note that all contributions to ZhangLabWiki may be edited, altered, or removed by other contributors. If you do not want your writing to be edited mercilessly, then do not submit it here.
You are also promising us that you wrote this yourself, or copied it from a public domain or similar free resource (see
ZhangLabWiki:Copyrights
for details).
Do not submit copyrighted work without permission!
Cancel
Editing help
(opens in new window)
Navigation menu
Personal tools
Not logged in
Talk
Contributions
Create account
Log in
Namespaces
Page
Discussion
English
Views
Read
Edit
View history
More
Search
Navigation
Main Page
Current events
Recent changes
Random page
Investigators
Matt Cai
Song Chen
Eric Chu
Dinh Diep
Elizabeth Duong
Shicheng Guo
Alan Fung
Daniel Jacobsen
Blue Lake
Huy Lam
Alice Li
Andrew Richards
Brandon Sos
Chris Wei
Yan Wu
Kun Zhang
Tools
What links here
Related changes
Special pages
Page information