Editing
EricChu:LabNotesMDA/2015-4-24
(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!
==Pair-End BWA on PGP1#21CoRE and GM20431-2Cell(Mar19)== * Chris helped me to make a batch file to run BWA sampe. The inputs are the two filenames per chamber in a single line in txt file (eg.EC-PGP1num21CoRE.txt). The outputs are sorted BAM and unique BAM files. * In /media/Syn_15T/Eric_15T/150422RapidRunPairEnd, vi create EC-PGP1num21CoRE.txt file, perl batch_bwa_pe_fastq2bam.final.pl EC-PGP1num21CoRE.txt hg19 > EC-PGP1num21CoRE.log vi create EC-GM20431-2C-Mar19.txt file, perl batch_bwa_pe_fastq2bam.final.pl EC-GM20431-2C-Mar19.txt hg19 > EC-GM20431-2C-Mar19.log * Get coverage statistics get_covstats.pl > EC_pairend_covstat.txt & /home/kunzhang/softwares/samtools-latest/samtools flagstat EC-GM20431-2C-Mar19-VI-30_S14_L001_R1_001.sorted.bam > EC-GM20431-2C-Mar19-VI-30_S14_L001_R1_001.sorted.bam.stat cat *.stat > flagstatall.log /home/kunzhang/softwares/samtools-latest/samtools flagstat EC-PGP1num21CoRE-Feb25-29_S37_L002_R1_001.sorted.unique.bam > EC-PGP1num21CoRE-Feb25-29_S37_L002_R1_001.sorted.unique.bam.stat2 cat *.stat2 > flagstatunique.log * Pileup Chr4 with combined VCFs of BAC and HiC /home/kunzhang/softwares/samtools-0.1.8/samtools pileup -Ac -f /GenomeDB/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa -l /media/LTS_33T/KZ_LTS33T/PGP1_BacPool/hapcut/vcfs/sorted.chr4.pgp1f_hg19_vcf_fixedCompleteGenomics_withHeaders_final-het-final.modifiedINFO3_clean_final.vcf EC-GM20431-2C-Mar19-III-17_S1_L001_R1_001.sorted.bam > EC-GM17_sorted_multialign_SNP.txt
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