User: cmdcolin

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cmdcolin330
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330
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Bioinformatics at MSU

Posts by cmdcolin

<prev • 74 results • page 1 of 8 • next >
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Comment: C: What Are The Most Common Stupid Mistakes In Bioinformatics?
... well, at the very least you may learn something that saves you an hour on a different project in the future ...
written 8 days ago by cmdcolin330
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Comment: C: biostars.org: Search capped to 50 hits?
... Don't mean to piggyback off this post but can you also sort by date? Seems neither classic nor the as-you-type search supports it ? ...
written 20 days ago by cmdcolin330
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Comment: C: Chip-seq on pooled replicates
... I think sometimes replicates do just get pooled so it's not out of the question, and many fewer programs exist for properly handling chip-seq replicates separately. the IDR pipeline from encode tried to tackle the problem ("Irreproducibility Discovery Rate") but it is probably just good to manually ...
written 4 weeks ago by cmdcolin330
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Comment: C: Convert bed12 to GFF
... I was checking out this file http://www.igbquickload.org/blueberry/V_corymbosum_Aug_2015/augustus-take6.bed.gz ...
written 5 weeks ago by cmdcolin330
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Comment: C: Convert bed12 to GFF
... I was able to get the BED_to_GFF app that I assume the raetsch lab created at the galaxy server here to work https://galaxy.inf.ethz.ch/ but it is corrupt (the children have same ID as parents) and outputs gtf/gff2 instead of gff3 ...
written 5 weeks ago by cmdcolin330
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Comment: C: Convert bed12 to GFF
... Hi there, I tried out genometools "gt bed_to_gff3 file.bed > out.gff" but it is giving a funny error about "gt bed_to_gff3: error: file "file.bed": line 116470: BED feature has length 0" but the file does not have a line 116470, it is only half that many lines. I dunno where to check for debuggin ...
written 5 weeks ago by cmdcolin330
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Convert bed12 to GFF
... There are several posts online about converting a GFF/GTF to BED12 but is there any way to go the other direction and convert BED12 to GFF? ...
bed gff bed12 written 5 weeks ago by cmdcolin330
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Comment: C: Split a BAM within a chromosome without losing read pairs
... It would be highly likely that name sorting it first and then splitting will be much much easier as pairs have the same name in a BAM file! ...
written 6 weeks ago by cmdcolin330
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Answer: A: Extracting entries from GTF file
... You may like to use tabix. Tabix has a setting that works well with GFF, so I would convert the GTF to GFF (probably using gffread from cufflinks package, for example `gffread -E merged.gtf -o- > merged.gff3`) Then you can bgzip and tabix the output bgzip myfile.sorted.gff tabix -p gff ...
written 8 weeks ago by cmdcolin330
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Comment: C: Perl::ForkManager does not speed up ATCG calculation !!
... note: I didn't mean to sound so negative and offtopic in this reply as I know the forkmanager was really the topic in question :) ...
written 8 weeks ago by cmdcolin330

Latest awards to cmdcolin

Commentator 3 months ago, created a comment with at least 3 up-votes. For C: How can an assembled genome have Ns in it?
Voter 3 months ago, voted more than 100 times.
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Jbrowse: importance of draw-basepair-track.pl
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: Jbrowse: importance of draw-basepair-track.pl
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: Jbrowse: importance of draw-basepair-track.pl
Scholar 2.3 years ago, created an answer that has been accepted. For A: Linking Jbrowse to Galaxy/Taverna
Scholar 2.4 years ago, created an answer that has been accepted. For A: Linking Jbrowse to Galaxy/Taverna
Supporter 2.5 years ago, voted at least 25 times.
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