User: dariober
dariober • 7.7k
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Posts by dariober
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... Correct me if I'm wrong but it may not be straightforward to apply htseq-count to gff3 (I don't know about featureCount). For typical differential gene expression, htseq-count needs an attribute that groups all the exons belonging to the same gene, the gene_id is usually the right one for gtf. But I ...
written 1 day ago by
dariober • 7.7k
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... Isn't it enough to keep reads without I or D operator in the cigar? For this you can use awk like:
samtools view -h in.bam chr1:12340-200000 \
| awk '$1 ~ "^@" || $6 !~ "I|D"' \
| samtools view -b - > out.bam ...
written 8 days ago by
dariober • 7.7k
3
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32
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... Well, since this old thread has been revived I cannot help promoting my own tool.
[ASCIIGenome][1] is a genome browser based on command line interface and designed for console terminals.
[1]: http://asciigenome.readthedocs.io/en/latest/description.html ...
written 9 days ago by
dariober • 7.7k
0
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... Are you sure the interval chr3:179198825-179199177 contains some reads? Make sure also that "chr3" is correct, maybe your chromosome is named "3". What is the output of `samtools view in.bam chr3:179198825-179199177`? ...
written 10 days ago by
dariober • 7.7k
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176
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Comment:
C: Setting up a lab wiki
... Interesting. I've been using GitHub for code and its markdown pages for documentation, similar to Ram's answer I guess. GitLab seems really interesting, do you have any particular reason to prefer it over GitHub?
About iRODS, I think/thought this was a pretty heavy weight solution, requiring a dedic ...
written 14 days ago by
dariober • 7.7k
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... +1 from me. One thing I like of FastQC is that it works with minimal input, just give it a fastq file and that's it. This comes at cost of simplistic output of course. Still I think it's important for a QC tool to require minimal configuration, or at least have default settings where all you need is ...
written 14 days ago by
dariober • 7.7k
3
votes
6
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357
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6
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... Sort of dodging the issue... Does your question really need hundreds of millions of records to be answered? If not, then you could consider downsampling the data and work with a smaller, random dataset that you can comfortably handle in R. If your analysis involves fitting a linear regression or ot ...
written 21 days ago by
dariober • 7.7k
0
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100
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... Watch out you have `"Mate End: "` but the code says `rec.getMateAlignment*Start*()` shouldn't it be `rec.getMateAlignmentEnd()`? Maybe try also to look at some read pairs in a genome browser to see where these numbers come from. ...
written 4 weeks ago by
dariober • 7.7k
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6.4k
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... Hi- If you want `xxxx.10` to come after `xxxx.2`, use the `--V/--version-sort` option in the sort command. ...
written 5 weeks ago by
dariober • 7.7k
1
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2
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221
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... I would like to link my answer to https://www.biostars.org/p/149538/ about the distinction (or lack thereof) between what are "technical" and "biological" replicates. ...
written 5 weeks ago by
dariober • 7.7k
Latest awards to dariober
Scholar
8 days ago,
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For A: Replace fields CHROM and POS in a vcf file
Teacher
9 days ago,
created an answer with at least 3 up-votes.
For A: plotting interactions in R with two data sets
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21 days ago,
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For A: count the number of transcription factor binding sites
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For A: plotting interactions in R with two data sets
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For Java Samtools Api: Write Bam To Stdout
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For A: plotting interactions in R with two data sets
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For A: plotting interactions in R with two data sets
Teacher
9 weeks ago,
created an answer with at least 3 up-votes.
For A: plotting interactions in R with two data sets
Scholar
9 weeks ago,
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For A: Replace fields CHROM and POS in a vcf file
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For A: plotting interactions in R with two data sets
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For C: Filtration Of Reads With Length Lower Than 30 From Bam
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For Picard API: Modify sam header
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For A: plotting interactions in R with two data sets
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For A: plotting interactions in R with two data sets
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For A: plotting interactions in R with two data sets
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For A: plotting interactions in R with two data sets
Scholar
5 months ago,
created an answer that has been accepted.
For A: Replace fields CHROM and POS in a vcf file
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5 months ago,
created an answer with at least 3 up-votes.
For A: plotting interactions in R with two data sets
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For A: Output the color code according to number
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For A: plotting interactions in R with two data sets
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For A: plotting interactions in R with two data sets
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