https://divingintogeneticsandgenomics.com/tags/samtools/ Recent content in Samtools on Chatomics Hugo -- gohugo.io en-us © 2018 Ming 'Tommy' Tang Thu, 10 Aug 2017 11:27:00 -0700 https://divingintogeneticsandgenomics.com/archive/bwa-mem-multi-mapping-reads/ Thu, 10 Aug 2017 11:27:00 -0700 https://divingintogeneticsandgenomics.com/archive/bwa-mem-multi-mapping-reads/ An error I was using TEQC to do quality control of my WES bam files aligned by bwa-mem. My data are paired end, so a function reads2pairs is called to make the paired-end reads to be a single fragment. I then get this error: > readpairs <- reads2pairs(reads) Error in reads2pairs(reads) : read pair IDs do not seem to be unique I asked in the bioconductor support site and went to the source code of that function. https://divingintogeneticsandgenomics.com/archive/downsampling-bam-files-to-a-certain-number-of-reads/ Thu, 05 May 2016 10:41:00 -0700 https://divingintogeneticsandgenomics.com/archive/downsampling-bam-files-to-a-certain-number-of-reads/ When compare different ChIP-seq data sets or analyze a set of ChIP-seq data sets together (e.g. ChromHMM analysis), it is desirable to subsample the deeply sequenced ones to a certain number of reads (say 15million or 30 million). In paper Integrative analysis of 111 reference human epigenomes: To avoid artificial differences in signal strength due to differences in sequencing depth, all consolidated histone mark data sets (except the additional histone marks the seven deeply profiled epigenomes, Fig. https://divingintogeneticsandgenomics.com/archive/rehead-a-bam-file/ Fri, 11 Apr 2014 12:00:00 -0700 https://divingintogeneticsandgenomics.com/archive/rehead-a-bam-file/ I downloaded some ChIP-seq bam files from the UCSC genome browser http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibTfbs/ and I found some bam files headers are without chrY information samtools view -H my.sorted.bam @SQ SN:chr1 LN:249250621 @SQ SN:chr2 LN:243199373 @SQ SN:chr3 LN:198022430 @SQ SN:chr4 LN:191154276 @SQ SN:chr5 LN:180915260 @SQ SN:chr6 LN:171115067 @SQ SN:chr7 LN:159138663 @SQ SN:chr8 LN:146364022 @SQ SN:chr9 LN:141213431 @SQ SN:chr10 LN:135534747 @SQ SN:chr11 LN:135006516 @SQ SN:chr12 LN:133851895 @SQ SN:chr13 LN:115169878 @SQ SN:chr14 LN:107349540 @SQ SN:chr15 LN:102531392 https://divingintogeneticsandgenomics.com/archive/count-how-many-mapped-reads-in-a-bam-file/ Tue, 18 Jun 2013 19:09:00 -0700 https://divingintogeneticsandgenomics.com/archive/count-how-many-mapped-reads-in-a-bam-file/ I wanted to count how many mapped reads are in a ChIP-seq bam file downloaded from UCSC ECODE project. http://genome.ucsc.edu/ENCODE/downloads.html A quick google search: http://left.subtree.org/ and http://seqanswers.com/forums/showthread.php?t=891 The output from short read aligners like Bowtie and BWA is commonly stored in SAM/BAM format. When presented with one of these files a common first task is to calculate the total number of alignments (reads) captured in the file. In this post I show some examples for finding the total number of reads using samtools and directly from Java code.