User: Macspider
Macspider • 2.5k
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Posts by Macspider
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... Both Devon and Genomax are right, because - at least my personal experience - it depends on your analysis.
Are you running an analysis composed of different replicates/accessions/genomes/species, or are the data coming from one source and one replicate?
- Many sources: add read groups that make ...
written 2 days ago by
Macspider • 2.5k
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... > Error details: SAM file doesn't have any read groups defined in the header. The GATK no longer supports SAM files without read groups
Your sam file doesn't have read groups. This is a common issue with GATK, as the program now wants the reads to be grouped for analysis purposes.
You can ass ...
written 2 days ago by
Macspider • 2.5k
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... If you isolate the read names of all the reads that have mapped, and then `sort | uniq` them, how many do you get? Chances that a multi-positional alignment is happening? ...
written 3 days ago by
Macspider • 2.5k
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... If you found my answer useful, upvote + mark it as answer, so the thread gets the "answered" status. (not because it's mine, just because it works like this here :D) ...
written 3 days ago by
Macspider • 2.5k
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... You also declare twice the `--star` argument in RSEM. That shouldn't be a problem, but since it seems that you're not super-solid on your command writing, perhaps check if every file you declare is in the folder you want it to be, check if every tag you added is exactly as it should be, and stuff li ...
written 3 days ago by
Macspider • 2.5k
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... Have a look at [GO.db][1].
In this R package, you can easily get PARENT, OFFSPRING and CHILDREN terms from a specified GO term.
[1]: https://bioconductor.org/packages/release/data/annotation/html/GO.db.html ...
written 3 days ago by
Macspider • 2.5k
1
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1
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... Is it normal that you have the same file specified in two arguments?
`-o clean_2.fq.gz -O clean_2.fq.gz` ...
written 3 days ago by
Macspider • 2.5k
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... Hi guys,
I am not completely sure this question fits Biostars (if not: please point me to the right discussion forum!).
I have generated a phylogenetic tree as a "consensus" of ~32,000 trees, each made from a different gene when compared with other species in a list I have.
As the consensus tr ...
written 7 weeks ago by
Macspider • 2.5k
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Comment:
C: Technical replicates in RNAseq
... Comparative Genomics @ CRG, Barcelona
http://www.crg.eu/en/toni_gabaldon ...
written 7 weeks ago by
Macspider • 2.5k
1
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Comment:
C: Technical replicates in RNAseq
... The new comment in this discussion just made me realize that we had this thread ~10 months ago here, and now me and @grant are sitting next to each other in the same lab. XD
Science: it's a small world!
Apart from that, maybe it would be interesting to tell the readers what, in the end, you did w ...
written 7 weeks ago by
Macspider • 2.5k
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