User: s1667153

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s16671530
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Posts by s1667153

<prev • 4 results • page 1 of 1 • next >
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How does BWA MEM know where to put X and Y origin reads correctly?
... Hi, I have recently been using BWA MEM to align 150bp paired-end reads from 2 cell lines, one is derived from a human male (XY) lineage and the other a female (XX). In the XY case I have reads aligning to both chromosomes, and in the XX case, only to X. How does the algorithm know to align reads a ...
bwa mem alignment genetics genomics written 7 months ago by s16671530 • updated 7 months ago by WouterDeCoster42k
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Use AWK to interrogate one file through another rather than for and while loops
... Hello, I have two files, 1 containing sequencing reads in a SAM like format, and the other contains the exon positions for HG38 and I am trying to use the positions of the exons in the second file to say whether a read in my first file is exonic or not. For ease Im a only using reads for chromosom ...
forloop else awk if exons written 8 months ago by s16671530
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Comment: C: extracting the exons coordinates on hg38
... Hi Bogdan I don't know whether you completed this in the end, but ffor anyone else who is trying to use Hg38 then I would recommend following the blog post linked above for hg19, but use the GENCODEv29 track instead of UCSC genes to download the canonical transcripts and exons file. Follow the in ...
written 8 months ago by s16671530
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Comment: C: Identify gene symbols given a list of chromosome positions
... Hi alex! I'm wanting to do something similar but I only have the start site position in my sorted BED file e.g. ``` chr1 9061386 chr1 9061390 ... ``` it has about ~20 lines, unfortunately my system doesn't have the most up to date version of gcc req'd for BEDOPS installation... is there another w ...
written 15 months ago by s16671530

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