User: finswimmer77

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finswimmer77120
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Posts by finswimmer77

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Comment: C: How to convert .vcf files into .csv?
... Hi, how should your mysql datatable look like? As in the vcf file the columns are tab-seperated you allready have a format you can import via phpmyadmin. But if you want to spilt the several fields in the INFO column, more work is needed. fin swimmer ...
written 1 hour ago by finswimmer77120
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Comment: C: pythonic way to get gene_id, gene_symbol from given list of gene, transcript co-
... Hello, you could use ensembl's [REST-Api][1] for this, e.g. the Overlap endpoint. fin swimmer [1]: http://rest.ensembl.org ...
written 5 days ago by finswimmer77120
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Comment: C: Faster way to get coverage per base
... I didn't try sambamba until now. But I recognize that picards CollectHsMetrics have an PER_BASE_COVERAGE option. As I'm running CollectHsMetrics in any case I could use this option. fin swimmer ...
written 18 days ago by finswimmer77120
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Comment: C: Understanding Picards HsMetrics
... Hello Pierre, that makes it a little bit clearer. So ON_TARGET means here only those bases of read which are realy mapped to a target position, and ON_BAIT counts also those bases that are not strictly mapped to a reference position but "somewhere between" (insertions) or are clipped? Is the ratio ...
written 18 days ago by finswimmer77120
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Understanding Picards HsMetrics
... Hello, I have some problems understanding the output of picards CollectHsMetrics. Because I don't have a bait file i uses my bed file with the target regions to produce the interval list. java -jar picard.jar BedToIntervalList I=target.bed SD=genome.dict O=target.interval_list This target int ...
picardtools bam sam written 19 days ago by finswimmer77120 • updated 19 days ago by Pierre Lindenbaum92k
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Comment: C: Faster way to get coverage per base
... Hello Titus, this is what I meant with > I can speed it up by dividing the bed file and start parallel processes. But it still needs about 45min to complete. :) ...
written 29 days ago by finswimmer77120
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Comment: C: Faster way to get coverage per base
... Could test it yesterday and it works with the -sorted option much faster than with samtools. Thanks a lot. fin swimmer ...
written 29 days ago by finswimmer77120
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Comment: C: Faster way to get coverage per base
... pileup.sh seems to need lot of memory which I have to little (around 6GB) :( The bed file is just needed to truncate the bam file to the region of interest. If I can pipe to pileup I can do this before with samtools view. So can I? Didn't find it in the documentation. fin swimmer ...
written 4 weeks ago by finswimmer77120
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Comment: C: Faster way to get coverage per base
... Should there be any reasonable differences to split the bam file and not the bed file with the regions of interests? I thought with the bam index it should be possible to have random access directly to the regions? fin swimmer ...
written 4 weeks ago by finswimmer77120
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Comment: C: Faster way to get coverage per base
... Never heard about sambamba before, but I will try it. fin swimmer ...
written 4 weeks ago by finswimmer77120

Latest awards to finswimmer77

Commentator 19 days ago, created a comment with at least 3 up-votes. For A: sam file error
Scholar 5 weeks ago, created an answer that has been accepted. For A: How to merge multiple bam files into single bam file
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: How to merge multiple bam files into single bam file

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