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Answer: gtf file for canFam2 genome version
by
Pierre Lindenbaum
165k
I wrote https://jvarkit.readthedocs.io/en/latest/KgToGff/
It was just a one-shot, I don't have used it much. Please check the results.…
Comment: Arioc (read mapping) ref sequence length error
by
Michael
•
0
Thanks for looking into that!
Yes, the aligner does indeed calculate the lengths. FYI, the .cfg file I posted above was produced by the…
Comment: Question about an alignment
by
swbarnes2
14k
Okay, it's not throwing it away, it's making the supplementary alignment 106 bases away, instead of counting it as a single alignment with …
Comment: gtf file for canFam2 genome version
by
1769mkc
★
1.2k
yes I'm looking for this canFam2 only that for some specific cases I have to use, even though I have the newer version also
Answer: Bioinformatics
by
Mensur Dlakic
★
29k
STRING works with derived data, which means they don't do any analyses on their own. You may get some information by clicking on links with…
Comment: Absolute vs. differential gene expression - which analysis is more informative?
by
Mensur Dlakic
★
29k
I don't think you will find a single person on this forum who will advocate for absolute expression analysis. In fact, almost the same ques…
Comment: Reproducibility Crisis
by
Mensur Dlakic
★
29k
This pretty much covers all the common reasons. I will add an anecdote to further illustrate the difficulty. Not too long ago I was trainin…
Comment: gtf file for canFam2 genome version
by
GenoMax
150k
Are you specifically looking for `canFam2`? Likely because newer versions available now: https://www.ncbi.nlm.nih.gov/datasets/genome/?taxo…
Answer: Reproducibility Crisis
by
GenoMax
150k
> What could be the reasons for this?
Many. At a minimum not using the same exact versions of software, command line options, input data e…
Comment: Question about an alignment
by
GenoMax
150k
> bwa is making the alignment work by throwing away half the read.
We don't know that based on the info above. It looks like out of the 13…
Comment: does any licenses needed to make experiments?
by
Dunois
★
2.9k
If you are a vegan and you have never even hurt a bug, then do not start hurting your fellow non-human beings now.
Comment: Question about an alignment
by
swbarnes2
14k
So CLC is making the alignment work by inserting a big gap, and bwa is making the alignment work by throwing away half the read. I'm incli…
Comment: Strange overrepresented sequence
by
georomano
•
0
I did see that one. I do wonder why these seqs would be over-represented in R2 and not R1... anyhow, as all of you mention, I will go ahead…
Comment: Strange overrepresented sequence
by
ATpoint
87k
Seconding this. Please don't overinterpret these fastqc results. It's really just a crude QC check. Go along with your analysis.
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