User: steve

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steve40
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Posts by steve

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Comment: C: Problem With Picard Dedup In Illumina Alignment Pipeline
... Same problem here with ReorderSam in 1.97. Picard 1.88 seems to work fine. Strange. ...
written 4.2 years ago by steve40
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Answer: A: Pindel Segmentation Fault (Version 0.2.4W)
... I encountered this exact error message a day or two ago. The issue for me was that the order of the BAM's @SQ lines (and thus the alignments, most likely) was different to the order of the chromosomes in the reference (genome) fasta file. Rather than re-order the BAM, it was much faster for me to c ...
written 4.2 years ago by steve40
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Comment: C: Bwa-Mem: Discriminate Between Reads Mapping Uniquely And Those Mapping In Multip
... MD can easily be added with samtools fillmd. But you're right though, others like SM:i are missing. ...
written 4.4 years ago by steve40
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Comment: C: Bwa-Mem - Where Has Sm:I Gone?
... So for BWA-MEM, is SM:i always equal to MAPQ? Is that why Heng removed this from the output? IF that's the case I can just duplicate the field. easy. ...
written 4.4 years ago by steve40
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Comment: C: Are Some Sequences Uniquely Mapped By Bwa When Mapped As Paired-End That Would N
... A follow up question has been posted here: BWA-MEM - Where has SM:i gone? ...
written 4.4 years ago by steve40
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Bwa-Mem - Where Has Sm:I Gone?
... This question is a follow up from: Are some sequences uniquely mapped by BWA when mapped as paired-end that would not be when mapped as single-end? My question is: How does BWA-MEM report single-end mapping quality? BWA-backtrack kindly reports the single-end mapping quality using the SM:i tag. B ...
samtools bwa written 4.4 years ago by steve40 • updated 4.4 years ago by Istvan Albert ♦♦ 75k
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Comment: C: Expanding Multiple Sequences In Fasta File
... Could you define 'expand' and perhaps elaborate on the first sentence of your question? ...
written 5.1 years ago by steve40
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Comment: C: How To Make Intervals In A Range Of Numbers?
... It's sounds like you're probably correct - you see, I don't have any experience with BED files or bedtools. However, I don't think the minor change that you've made to your awk command would work as intended. Did you test the code? ...
written 5.1 years ago by steve40
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Comment: C: How To Make Intervals In A Range Of Numbers?
... The only problem is that the next line is not offset from the last by one. You may want to re-check the expected output ...
written 5.1 years ago by steve40
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Answer: A: How To Make Intervals In A Range Of Numbers?
... I have followed this from here: http://stackoverflow.com/questions/13551174/how-to-make-intervals-in-a-range-of-numbers Here's one way using awk: awk -v num=100 '{ for (i=1;i<=$NF;i++) { print $1, $2, var=(i==$NF?$3:$2+=num), i, (var-$2==0?"100":var-$2); $2++ } }' file Results: chr1 37850 ...
written 5.1 years ago by steve40

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