I have a bam file with header such like this: @RG ID:S1-L001 LB:L001 PL:Illumina SM:L001 PU:novaSeq @RG ID:S1-L002 LB:L002 PL:Illumina SM:L002 PU:novaSeq This bam file …

Hi, I am using [samblaster][1] to mark duplicates, and it requires the reads to be read id sorted. Can anyone explain it? I have read …

<p>Hello,</p> <p>I have 10 fasta files with sequenced reads information with read sizes from 15 - 35 . I have combined the reads and collapsed …

<p>Hi,</p> <p>I did a search looking for the best definitive way to fill up @RG information in a <a href='http://samtools.sourceforge.net/SAM1.pdf'>BAM</a> file. This is what I …

<p>Hi, All</p> <p>I was trying to use seqtk to randomly pickup 32,000,000 sequences from my sequence pool.</p> <p>I first combined all of sequences from two …

<p>Hi, there</p> <p>I was trying to add read groups to my alignments and take advantage of GATK to call variants. I first did my cleaned …

<p>Do the sequences in <a href='http://samtools.sourceforge.net/SAM1.pdf'>SAM</a>/BAM header have to match the number and the order of the sequences in reference FASTA file?</p> <p>For example, if …

<p>Hi all, I get an GATK error </p> <pre><code>SAM/BAM file SAMFileReader{/merged_bam_markdup.bam} is malformed: Read HWI-ST303_0093:5:5:13416:34802#0 is either missing the read group or its read group …

<p>I get this error when trying to make a database from fasta file:</p> <pre><code>BLAST options error: blastdb.FASTA does not match input format type, default input …

<p>From <a href="http://biostar.stackexchange.com/questions/1389/how-to-generate-a-consensus-fasta-sequence-from-sam-tools-pileup">http://biostar.stackexchange.com/questions/1389/how-to-generate-a-consensus-fasta-sequence-from-sam-tools-pileup</a> We use awk and perl to get fasta by</p> <pre><code>awk '/^@chr1$/,/^+$/' consensus.fastq | perl -pe "s/@/&gt;/ ; s/\\+//" &gt; chr1.fasta </code></pre> <p>The …