https://divingintogeneticsandgenomics.com/tags/bowtie/ Recent content in Bowtie on Chatomics Hugo -- gohugo.io en-us © 2018 Ming 'Tommy' Tang Fri, 07 Jun 2013 13:51:00 -0700 https://divingintogeneticsandgenomics.com/archive/remap-the-eland-sorted-txt-file-from-hg18-to-hg19/ Fri, 07 Jun 2013 13:51:00 -0700 https://divingintogeneticsandgenomics.com/archive/remap-the-eland-sorted-txt-file-from-hg18-to-hg19/ Sometime ago, I wrote a blog about how to convert Eland sorted.txt file to bam file convert Eland sorted.txt to bam file the original Eland file was mapped to hg18, but I want to remap it to hg19. essentially, I need a fastq file to map it by bowtie. A quick google search: http://seqanswers.com/forums/showthread.php?t=7061 so, the bamtools https://github.com/pezmaster31/bamtools (yes, github again...that's why I want to learn git a little bit, see my last post My first try on Git) https://divingintogeneticsandgenomics.com/archive/sra-file-and-my-first-bowtie-run-on-uf-hpc-high-performance-computing-center/ Tue, 07 May 2013 09:30:00 -0700 https://divingintogeneticsandgenomics.com/archive/sra-file-and-my-first-bowtie-run-on-uf-hpc-high-performance-computing-center/ I wanted to have a look at a certain ChIP-seq data in MCF7 breast cancer cells. I could not find any data sets in UCSC which are in bam file format. then, I found a sra file in NCBI sequence read archive: http://www.ncbi.nlm.nih.gov/sra I downloaded the sra file from there, next question would be : how to convert it to sam or bam file? It looks like SAR toolkit http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=toolkit_doc&f=std#header-globalcan directly convert sra to bam file combined with samtools.