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Comment: Output file of satools flagstat empty
by
GenoMax
142k
If you posted the entire command line then you did not include `-O $MAPPING/${i}.mapping_stats.txt`
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=1,Type=Strin…
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…
Comment: Adata.raw.X in LIANA, something wrong with conversion from Seurat to adata in py
by
beginner123
•
0
Hi, no I'm using the python implementation as linked above.
Comment: joint callset and vcf sorting, unknown TAG issue
by
Pierre Lindenbaum
161k
Show us the content of the INFO column at the problematic positions.
Comment: Tissue-specific DEG analysis with DEseq2
by
ATpoint
82k
Sounds like full confounding. Be careful. Personally I would not do this comparison. There is no way to distinguish tissue effect from dono…
Answer: input file in rmats
by
Mathew
▴
90
Hi,
In the example they give in their GitHub (https://github.com/Xinglab/rmats-turbo/blob/v4.3.0/README.md):
They have 2 sample groups wi…
Comment: Longest transcript variant per gene
by
Mathew
▴
90
I'm glad it worked well for you! Good luck with the rest of your project. I wish you the best.
Comment: Longest transcript variant per gene
by
sansan_96
▴
90
Hello again,
It works very well, thank you very much for this solution.
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