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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
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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
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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
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vernonlim98
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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
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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
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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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You assembled a genome using samtools ???? that sounds very weird, if not impossible ...
The header (SQ lines) is missing from your file b…
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benformatics
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The XX and XY counts are present on any given variants page.
Comment: Help with Ideathon
by
Mensur Dlakic
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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
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ATpoint
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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
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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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