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Recent Replies
Comment: How to create a consensus of a contig with samtools or bbmap?
by
lieven.sterck
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great to hear!
and yes, spades in stead of samtools makes much more sense :-)
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> align_ch returns tuples like [sample_name, [read1, read2]]. I want aligned_input tuples to look like [index_dir, sample1, read1, read2].
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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?
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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?
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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:
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$ …
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> $ gff3-to-tbl .../pharokka.gff .../Annotation/pharokka_cds_final_merged_output.tsv .../Consensus/reference.fasta .../Annotation/phanotate…
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> Could this be an issue caused by the sequencing facility or just that they are in fact out of sync?
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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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These are the 2 papers I mentioned previously that used data other than raw counts for their analysis: https://onlinelibrary.wiley.com/doi/…
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Hello German , I am using clinCNV for WES and i faced the same error and this part of the error
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sorry, I have mistaken samtools with spades... running `samtools view -h...` did the trick. Thank you.
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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…
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You assembled a genome using samtools ???? that sounds very weird, if not impossible ...
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The XX and XY counts are present on any given variants page.
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