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Recent Replies
Comment: How do I get description in BLAST?
by
Riku
▴
60
I share some of results.
It means partial N/A is displayed.
$ head results
TRINITY_DN3139_c0_g2_i2 transcript=K12D12.2.1 gene=WBGe…
Answer: How to write a Python script to edit a .vcf file?
by
sbstevenlee
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200
You may want to check out the `pyvcf` [submodule](https://sbslee-fuc.readthedocs.io/en/latest/api.html#module-fuc.api.pyvcf) I wrote (it's …
Comment: How do I get description in BLAST?
by
lieven.sterck
12k
with exactly do you mean with " shows a lot of N/A " ? That you don't get any hit or that there is no usable functional description for the…
Comment: What is eggnog better than previous annotation in terms of?
by
Riku
▴
60
I got it.
I understood this very easily.
Thank you very much for your kind explanation!
Comment: Mean Length Of Fasta Sequences
by
cicindel
▴
70
And now I noticed this solution uses basically the same logic as [Lars' answer][1] above :/
[1]: https://www.biostars.org/p/1758/#1795
Comment: How to understand logics and statistical concepts behind limma package?
by
Papyrus
★
1.5k
Wow, those posts/ebook by David Robinson are great!! thanks for sharing!
Comment: Mean Length Of Fasta Sequences
by
cicindel
▴
70
Initially, I tried to implement the same idea with `grep` and `wc`, but the number I got was off (higher by a few dozen). Then I remembered…
Comment: What is eggnog better than previous annotation in terms of?
by
lieven.sterck
12k
As said, I'm not familiar with the details of eggNOG but I would assume something like that indeed.
Answer: Mean Length Of Fasta Sequences
by
cicindel
▴
70
# The (M)AWK way
Using a modified 2nd example from `mawk` [manual][1]:
awk '
/>/ {nseq++}
!/>/ {chars += length($0)}
…
Answer: How to understand logics and statistical concepts behind limma package?
by
i.sudbery
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As noted by @papyrus, until you understand linear models, you are going to struggle to understand limma. So start there. If you don't get o…
Comment: What files (fasta, GTF) do I need for RNA seq analysis
by
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Yes, If you use genome based method ,you can use subjunc to align fastq to your Genome and use featurecount to quantify read counts, at thi…
Answer: Do we need to filter out the 0 counts sgRNA in CRISPR analysis?
by
xiaoguang
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Are you doing crispr_screening? I know that the software mageck will remove 0 read sgRNA firstly
Comment: Kmergenie module readfq not found
by
imogen.dumville
•
0
How would you do this? I'm new to downloading modules and don't see an obvious tar download file on their github.
Comment: How to cluster existing multiple sequence alignments to identify homologous clus
by
lieven.sterck
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I see, perhaps you can first run a simple blast and run blastclust or such on the results to get a rough clustering ?
Answer: Open source python tool for convert VCF files to JSON?
by
4galaxy77
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990
This looks like what you would need:
https://github.com/gchatterjee-git/VCF-to-JSON-Parser
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