User: Macspider
Macspider • 2.4k
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Posts by Macspider
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... Hi guys,
Does anyone of you have experience with computing the variant distance bias (VDB) value for VCF-formatted files?
I am trying to figure out myself how to do it, but literature / documentation / discussion on it is quite scarce.
So far, what I know is:
- The higher the value, the bigg ...
written 6 days ago by
Macspider • 2.4k
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... Impute with which tool? What is your reference file format? What are MSL individuals? ...
written 7 days ago by
Macspider • 2.4k
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... Hello guys,
Title is pretty self-explanatory: what is the quickest way to convert the output of command line blast (say xml format, but I'm open to any suggestion) to a pseudo-VCF file?
I am interested in getting all the positions where I have a SNP (mismatch) between query and subject. Doesn't ...
written 19 days ago by
Macspider • 2.4k
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Comment:
C: building index with HISAT2
... Each reference has to have its own index. You are currently loading many references (i.e. all the fasta files you have as comma-separated) and sending them to one only reference basename (hisat_index).
If you have, say, three reference sequences named 1.fa, 2.fa and 3.fa, your command should have ...
written 27 days ago by
Macspider • 2.4k
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... I am having the same problem in this moment, did you manage to solve it? If yes, how? ...
written 28 days ago by
Macspider • 2.4k
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131
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Answer:
A: building index with HISAT2
... You're specifying the path only for the first file:
`/data/memona/reference/`
Move into that directory and then run hisat2 without the path specification.
Also, as fair as I know, you have to specify as many index basenames as there are input files, the same way (comma separated). ...
written 28 days ago by
Macspider • 2.4k
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99
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... Check if you have an empty line at the beginning / end of the file. ...
written 4 weeks ago by
Macspider • 2.4k
0
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107
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1
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Answer:
A: strange htseq-count result
... > -s no
This is (imho) the problem. Perhaps your library is stranded. I'm saying this because I see ~ half of the scores in __no_feature and another half in __ambiguous. Try `-s yes`! ...
written 4 weeks ago by
Macspider • 2.4k
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... Actually, it is not exactly as you said:
> one contains calls on the whole genome, the other contains an subset of it
I don't have a non-CDS group and a CDS group, I have a whole-genome (including CDS) and a CDS only.
Also, I am quite confident on the annotation because it was done by me, so ...
written 4 weeks ago by
Macspider • 2.4k
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... Hello guys, I am working with rates of variation (expressed in SNP/Mbp) and I'm observing something which biologically doesn't have much sense.
I have two variant call sets: one contains calls on the whole genome, the other contains an subset of it, made on the coding regions only (CDS lines in GF ...
written 4 weeks ago by
Macspider • 2.4k
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