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Recent Replies
Comment: How to convert gff to Sequin format with gff3-to-tbl?
by
GenoMax
154k
So should your command not be (assuming these are the right files) ?
$ gff3-to-tbl .../pharokka.gff .../Annotation/pharokka_cds_final…
Comment: How to convert gff to Sequin format with gff3-to-tbl?
by
marongiu.luigi
▴
760
ADDENDUM: I have seen that pharokka already provides a tbl file; anyway, the question remains: if I needed to convert a gff to sequin with …
Comment: How to convert gff to Sequin format with gff3-to-tbl?
by
marongiu.luigi
▴
760
Thank you, I have updated the title as suggested. But in the command, there a gff, a tsv, and a protein fasta. The list of files is:
```
$ …
Answer: How to convert gff to Sequin format?
by
GenoMax
154k
> $ gff3-to-tbl .../pharokka.gff .../Annotation/pharokka_cds_final_merged_output.tsv .../Consensus/reference.fasta .../Annotation/phanotate…
Comment: Errors with RSEM/bowtie2
by
GenoMax
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> Could this be an issue caused by the sequencing facility or just that they are in fact out of sync?
We have no way to know. Did the sequ…
Comment: Differences between published differential gene expression results and own analy
by
vernonlim98
•
0
Have included the links to the papers I mentioned in another comment for reference!
Comment: Differences between published differential gene expression results and own analy
by
vernonlim98
•
0
These are the 2 papers I mentioned previously that used data other than raw counts for their analysis: https://onlinelibrary.wiley.com/doi/…
Comment: Collect COV file by BedCoverage
by
eshrakaali_p
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Hello German , I am using clinCNV for WES and i faced the same error and this part of the error
[1] "ERROR: your file with normal cove…
Comment: How to create a consensus of a contig with samtools or bbmap?
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marongiu.luigi
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sorry, I have mistaken samtools with spades... running `samtools view -h...` did the trick. Thank you.
Comment: Help with Ideathon
by
V K
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Thank you for the response! Unfortunately this is completely independent and not part of a course. I was asking for some innovative ways to…
Answer: How to create a consensus of a contig with samtools or bbmap?
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lieven.sterck
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You assembled a genome using samtools ???? that sounds very weird, if not impossible ...
The header (SQ lines) is missing from your file b…
Answer: gnomad par region variants
by
benformatics
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The XX and XY counts are present on any given variants page.
Comment: Help with Ideathon
by
Mensur Dlakic
★
30k
I don't see a single question here. Saying `I need your expert help in figuring out how I can make this analysis useful!` is too open-ended…
Comment: Differences between published differential gene expression results and own analy
by
ATpoint
89k
Please link the paper, lets see their methods. With human data it can well be that they included something like surrogate variables to damp…
Comment: Differences between published differential gene expression results and own analy
by
dsull
★
7.7k
There are many ways to do normalization and one of the correct ways is simply to plug raw counts into deseq2 (the math that deseq2 uses to …
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