User: ccnn

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ccnn10
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Posts by ccnn

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Comment: C: No Sequencing Data at Low Positions
... Got it. Thank you! So is there somewhere I can find out how many of the first bases of each chromosome are N? ...
written 4 months ago by ccnn10
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Comment: C: No Sequencing Data at Low Positions
... Ah it does indeed like everything before that is "N" when I zoom into "base" on the browser. ...
written 4 months ago by ccnn10
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Comment: C: No Sequencing Data at Low Positions
... I think so. http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&lastVirtModeType=default&lastVirtModeExtraState=&virtModeType=default&virtMode=0&nonVirtPosition=&position=chr22%3A16049522-16050522&hgsid=662132401_e7mUocboTcIMiTPiqCEGpqCVAIpq 22 is only 51304566 bp long. So t ...
written 4 months ago by ccnn10
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No Sequencing Data at Low Positions
... Opening a bam file for just chr22, I was surprised to see that there were no reads aligned until around position 16,050,000. In UCSC Genome Browser, looking at a window of chr22:16,049,420-16,050,420, I can see that there's "nothing," but then different tracks start. In chr1, I also think I remember ...
dna ngs next-gen sequencing written 4 months ago by ccnn10
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Answer: A: Where to Download ExAC pLI Scores
... Ah, I found it at ftp://ftp.broadinstitute.org/pub/ExAC_release/release1/manuscript_data/forweb_cleaned_exac_r03_march16_z_data_pLI.txt.gz ...
written 4 months ago by ccnn10
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Where to Download ExAC pLI Scores
... I can look up any gene in the ExAC browser and find its pLI score (described [here][1]) in the LoF row. But I haven't been able to find a file that I can download that lists the pLI scores for every gene for which ExAC's calculated it. Is this data available somewhere? [1]: https://www.nature. ...
genome sequencing written 4 months ago by ccnn10 • updated 12 weeks ago by gniyuhz0
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Does bamtools split preserve sort and rmdup?
... Taking over someone else's code, I've discovered a bottleneck. This is a portion of a script that accepts a BAM and outputs smaller, sorted, rmdup-ed, indexed BAMs for each chromosome. for chr in 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y M; do samtools view ...
genome alignment samtools bamtools bam written 6 months ago by ccnn10 • updated 6 months ago by Devon Ryan82k

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Scholar 4 months ago, created an answer that has been accepted. For A: Where to Download ExAC pLI Scores

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