https://divingintogeneticsandgenomics.com/tags/bam/ Recent content in Bam on Chatomics Hugo -- gohugo.io en-us © 2018 Ming 'Tommy' Tang Thu, 05 May 2016 10:41:00 -0700 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/convert-bam-to-fastq-and-remap-it-with-bwa-mem/ Tue, 06 Oct 2015 15:21:00 -0700 https://divingintogeneticsandgenomics.com/archive/convert-bam-to-fastq-and-remap-it-with-bwa-mem/ Why we want to revert bam files back to fastq file? Sometimes, you get a processed bam file from other resources, but you want to map it with another aligner. For example, the old BWA aln does not keep the information for soft-cliped reads which are useful for structural variant detection, the new BWA mem is more suitable for this. So, I want to dump bam to fastq first and then realign it with BWA MEM. https://divingintogeneticsandgenomics.com/archive/convert-bam-file-to-bigwig-file-and-visualize-in-ucsc-genome-browser-in-a-box/ Thu, 23 Oct 2014 13:13:00 -0700 https://divingintogeneticsandgenomics.com/archive/convert-bam-file-to-bigwig-file-and-visualize-in-ucsc-genome-browser-in-a-box/ I just came across UCSC genome browser in a box Gbib, and I want to try it out. what is Gbib? from the link above: "Genome Browser in a Box (GBiB) is a "virtual machine" of the entire UCSC Genome Browser website that is designed to run on most PCs (Windows, Mac OSX or Linux). GBiB allows you to access much of the UCSC Genome Browser's functionality from the comfort of your own computer. 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. https://divingintogeneticsandgenomics.com/archive/convert-eland-sorted-txt-to-bam-file/ Sat, 01 Jun 2013 16:40:00 -0700 https://divingintogeneticsandgenomics.com/archive/convert-eland-sorted-txt-to-bam-file/ I downloaded a human ChIP-seq data set mapped to hg18 from NCBI GEO. it is in Eland sorted.txt format, I want to convert it to bam file for some downstream analysis. a google search: http://www.biostars.org/p/3121/ I followed the link to http://genomewiki.ucsc.edu/index.php/ABRF2010_Tutorial the export2sam.pl script in the samtool is what I need. I downloaded samtools-0.1.8 and found the script in the misc folder. but I got errors when I tried to convert it: