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Recent Replies
Answer: Tissue-specific DEG analysis with DEseq2
by
arctic
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40
Not my area of expertise but GTEx portal seems to offer visual comparison of expression across tissues, maybe checking their pipeline could…
Comment: Is it Possible to "Merge" data from Replicates within a VCF SNP File
by
Pierre Lindenbaum
161k
> I think I am mostly struggling with what would need to be coded to my dataset here and how to run this loop on my set in general.
i do…
Comment: Is it Possible to "Merge" data from Replicates within a VCF SNP File
by
ajbarrett98
•
0
Pierre,
I am a novice at all of this in general and I have never used Java-based programming before. I may not be able to properly wrangl…
Answer: Practical Haplotype Graph v2 not finding correct paths
by
pjb39
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200
There have been a couple of bugs found that affect imputation accuracy, one in build-kmer-index and one in find-paths. The find-paths bug o…
Comment: Output file of satools flagstat empty
by
Mathew
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90
Hi,
In your samtools flagstat, -o specifies the output format. This can be set to 'default', 'json', or 'tsv'. If -o is not specified , t…
Comment: Tissue-specific DEG analysis with DEseq2
by
BioinfGuru
★
1.7k
I wrote an R package (see [rrdr.io][1], and [github][2]) some years ago to calculate tissue specificity from bulk RNAseq based on [this pap…
Comment: joint callset and vcf sorting, unknown TAG issue
by
Pierre Lindenbaum
161k
> set the Number= to 0 instead of 1;
I'm not sure it's a problem.
> probably I should also change the Type to Flag
ah yes, my bad ! (f…
Comment: Output file of satools flagstat empty
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GenoMax
142k
If you posted the entire command line then you did not include `-O $MAPPING/${i}.mapping_stats.txt` in that.
Comment: joint callset and vcf sorting, unknown TAG issue
by
Matteo Ungaro
▴
100
@Pierre Lindenbaum I see. I looked up and, although present, the TAG goes like this in both files:
`##INFO=<ID=1000gALT,Number=0,Type=Flag,…
Comment: joint callset and vcf sorting, unknown TAG issue
by
Matteo Ungaro
▴
100
@Pierre Lindenbaum much appreciated, thanks for the explanation and possible approaches to solve this.
I'm not in the position to run `U…
Comment: Tophat multiple or unique mapping criteria
by
Ruqaiya
•
0
> The --b2-mp defines the mismatch penalty: the first number is used when the quality of the base is good, the second when it's bad. If you…
Comment: joint callset and vcf sorting, unknown TAG issue
by
Pierre Lindenbaum
161k
> Still, I can't understand the Invalid tag name: "1000gALT"
the following line is missing in the VCF header:
##INFO=<ID=1000gALT,Num…
Answer: joint callset and vcf sorting, unknown TAG issue
by
Pierre Lindenbaum
161k
INFO at 121387974 is
.;CpG
this is an invalid INFO column. There is an invalid attribute named '.' followed by the attribute CpG, …
Comment: joint callset and vcf sorting, unknown TAG issue
by
Matteo Ungaro
▴
100
@Pierre Lindenbaum as I don't know the meaning of `.;` and I've seen there are many in both files, I simply removed them with `grep -v`.
…
Comment: joint callset and vcf sorting, unknown TAG issue
by
Matteo Ungaro
▴
100
My bad I switched positions between the two files when looking the first time. They do indeed look abnormal but how can I fix it? Below the…
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