Hi All I was look at the `samtools mpileup` output format and found something odd in the reported quality scores. 1 633887 G 28 >><<<<CAAA.AA.AAAcaAAAC.A..a …

If not, is there a place where a BAM and its FASTA file can be found together? My program is designed to gather allelic frequencies …

I am trying to analyze reprocessed consolidated roadmap epigenome data and I have downloaded the data regarding H3K4ME1 in Male fetal brain from: http://egg2.wustl.edu/roadmap/data/byFileType/alignments/consolidated/E081-H3K4me1.tagAlign.gz but …

I have an old data from cufflinks, and this data is in the expr format. When searching the for the exprtogtc module that convert it …

I have checked the documenation here: http://samtools.sourceforge.net/pileup.shtml Here is an output of column 5 (read base column): ``` samtools view -h bamfile.bam | samtools mpileup …

<p>I'm having trouble extracting a <a href='http://samtools.sourceforge.net/pileup.shtml'>pileup</a> file from an <a href='ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX101/SRX101206/SRR364089/SRR364089.sra'>SRA</a> using <code>sra-pileup</code> command. NCBI <a href='http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=toolkit_doc&amp;f=sra-pileup'>documentation</a> only covers command line arguments for the …

<p>Hi I'm trying ReadDepth to call CNV. Anyone knows how to prepare the input Bed file from the <a href='http://samtools.sourceforge.net/SAM1.pdf'>BAM</a> file. There are only short …

<p>I have a few related questions on how ChIP-Seq transcription factor binding data from ENCODE, obtained via the UCSC website, should be interpreted. I'm trying …

<p>Hi,</p> <p>What does "~" (tilde) and "]" means in column 5 (base string) of the samtools pileup format? </p> <p>I cant seemed to find anything …

<p>SAM tools pileup produces a consensus sequence in vertical format, which is not terribly useful for traditional sequence analysis. Does anyone know of a command …