User: Pascal

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Pascal1.4k
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Posts by Pascal

<prev • 112 results • page 1 of 12 • next >
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Answer: A: How To Store Large Genome Sequence In Oracle Table?
... What datatype are you using in your table schema? Have you considered using CLOB data type as describe here ? ...
written 5.4 years ago by Pascal1.4k
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Answer: A: A Question About The Sam Entry For A Query Aligned To Multiple Places
... Ah that's funny because with my colleages we just calculated something similar. Have a look to the ratio a/b calculated on your sam file: a: samtools view [?] | sort | uniq | wc -l b: samtools view [?] | cut -f 1 | wc -l ...
written 5.4 years ago by Pascal1.4k
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Comment: C: How Reads Have Been Mapped In My Bam File?
... Regarding the X0, X1, this is a very good idea, but unfortunately it does not seem to be present (I assume, according to SAM format specifications that "X0" or "X1" might be present): samtools view NA12878.chrom1.SLX.maq.SRP000032.2009_07.bam | grep X0 ...
written 5.4 years ago by Pascal1.4k
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Comment: C: How Reads Have Been Mapped In My Bam File?
... No @PG in header. I had verified this point already. Thanks anyway. ...
written 5.4 years ago by Pascal1.4k
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How Reads Have Been Mapped In My Bam File?
... Working with 1000 Genome Project bam files (NA12878, pilot2), I'd need to know how the reads have been mapped and in particular if there are "unique mapping" for all these reads or if reads have multiple possible mapping. ...
alignment bam written 5.4 years ago by Pascal1.4k • updated 5.4 years ago by Vikas Bansal2.2k
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Comment: C: Fine Tune Ngs Downstream Analyses Using Genome Mappability ?
... FYI, you can download bigWigToBedGraph from http://hgdownload.cse.ucsc.edu/admin/exe/ ...
written 5.4 years ago by Pascal1.4k
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Answer: A: Fine Tune Ngs Downstream Analyses Using Genome Mappability ?
... Very interesting question. Regarding the bonus question, why don't you simply download it from this UCSC data download page (file wgEncodeCrgMapabilityAlign100mer.bw.gz maybe?). Use bigWigToBedGraph to convert it to bedGraph format. ...
written 5.4 years ago by Pascal1.4k
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Comment: C: What Ngs Read Simulators Are Available For Single-End 35Base Pair Length Data?
... Can you explain "mapping data is not as expected for small RNA data"? ...
written 5.4 years ago by Pascal1.4k
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Comment: C: Why Does Ucsc "Exons" Track Overlap With "Introns" Track?
... Excellent. Thank you so much for the explanation! ...
written 5.5 years ago by Pascal1.4k
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Why Does Ucsc "Exons" Track Overlap With "Introns" Track?
... I've downloaded BED files from UCSC Table Browser for the "Exons" track and for the "Introns" track. But I just discovered that these BED files have some overlaps ?! Could you please explain me where these overlap come from? ...
ucsc browser written 5.5 years ago by Pascal1.4k • updated 5.5 years ago by Malachi Griffith15k

Latest awards to Pascal

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Centurion 5.2 years ago, created 100 posts.
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Student 5.5 years ago, asked a question with at least 3 up-votes. For Why Does Ucsc "Exons" Track Overlap With "Introns" Track?
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