Editing
Matt:LabNotes/2014-8-1
(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!
==GenePattern: Tophat & RNA-SeQC== *Using genepattern.broadinstitute.org ===Tophat version 8.6=== *Upload files s_1_1_Indx26.txt s_1_1_Indx27.txt s_1_1_Indx28.txt s_1_1_Indx29.txt s_1_1_Indx32.txt *Bowtie index Homo_sapiens_hg19_UCSC *GTF file Homo_sapiens_GENCODE_hg19_v7_chr1_format.gtf *library type Standard Illumina (fr-unstranded) *quality value scale Solexa 1.3 (Phred 64) *output prefix <Indx##reads.pair.1_basename> *transcriptome only yes *'''left blank''': **transcriptome index **reads pair 2 **mate inner distance **mate std dev **all others not mentioned were left at default ====Alignment Summary==== *RanHex_Indx26 Reads: Input : 5441 Mapped : 3765 (69.2% of input) of these: 384 (10.2%) have multiple alignments (18 have >20) 69.2% overall read mapping rate. *dT_Indx27 Reads: Input : 10905 Mapped : 8444 (77.4% of input) of these: 838 ( 9.9%) have multiple alignments (65 have >20) 77.4% overall read mapping rate. *FISSEQRT_Indx28 Reads: Input : 7024 Mapped : 5018 (71.4% of input) of these: 629 (12.5%) have multiple alignments (58 have >20) 71.4% overall read mapping rate. *Top48_Indx29 Reads: Input : 12158 Mapped : 7220 (59.4% of input) of these: 801 (11.1%) have multiple alignments (72 have >20) 59.4% overall read mapping rate. *gDNA_Indx32 Reads: Input : 111950 Mapped : 55280 (49.4% of input) of these: 6418 (11.6%) have multiple alignments (1749 have >20) 49.4% overall read mapping rate. ===RNA-SeQC=== <!--====Picard.MergeBamAlignment==== *to add unaligned reads bam file to accepted --> ====Picard.AddOrReplaceReadGroups ver3==== *input file: accepted_hits.bam *read group id: Indx## *read group library: RTenrichmRNA *read group platform: Illumina *read group platform unit: ## (eg 26 for Indx26) *read group sample name: (eg RanHex_Indx26) *output prefix: accepted_hits_##RG ====SortSam ver4==== *input file: accepted_hits_##RG.rgroup.bam (output from previous step) *sort order: coordinate *output format: BAM *output prefix: accepted_hits_## ====SAMtools.FastaIndex ver1.2==== *fasta file: Homo_sapiens_UCSC_hg19.fa *output prefix: Homo_sapiens_UCSC_hg19 ====Picard.CreateSequenceDictionary ver1==== *reference sequence file: Homo_sapiens_UCSC_hg19.fa *truncate names at white space: yes *output file: Homo_sapiens_UCSC_hg19.dict ====Picard.ReorderSam==== *input file: bam from SortSam *reference file: fa from SAMtools.FastaIndex *reference sequence dictionary: Homo_sapiens_UCSC_hg19.dict from Picard.CreateSequenceDictionary allow partial overlap: no allow contig length discordance: no output prefix: accepted_hits_## ====Picard.MarkDuplicates==== *input file: reorder.bam from Picard.ReorderSam *remove duplicates: no *default everything *output prefix: accepted_hits_## ====SortSam==== *Update index *input file: .mdup.bam from Picard.MarkDuplicate *sort order: coordinate *output format: BAM *output prefix: accepted_hits_## ====RNAseqMetrics==== *bam files: zip of sorted.bam and sorted.bai files from SortSam *sample info file: <blank> *single end: yes *annotation gtf: Hg 19, GenCode,'chr1' format contigs *reference sequence: from SAMtools.FastaIndex *reference sequence index: from SAMtools.FastaIndex *reference sequence dictionary: from Picard.CreateSequenceDictionary *num genes: 1000 *transcript level metrics: no *rRNA interval file: <empty> *rRNA reference file index: zip from BWA.indexer of human_all_rRNA.fa ~/Genomes/RNA-SeqCResources/human_all_rRNA.fasta input to BWA.indexer ver1.8 in GenePattern (is algorithm) *gc content file: <empty> *output prefix: RTenrichmRNA
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