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Recent Replies
Answer: How to merge unique/non overlapping genes between 2 gene model GFF3 files?
by
jv
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`bedtools intersect -v` is one option for identifying the unique genes from the older gene model. <https://bedtools.readthedocs.io/en/lates…
Comment: DESeq2 results function runs very slow on Windows 10
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Does it go away if you remove the `parallel` from `results()`? After all, it is the `DESeq()` function that is the bottleneck when n is lar…
Comment: HTSeq error processing GFF file
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ibq.enriquepola
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enrique@L:~/bioinformatica/index/prueba$ head -n 997531 GCF_902167145.1_Zm-B73-REFERENCE-NAM-5.0_genomic.gff|tail -n 1
NC_007982.1 Ref…
Comment: Which file and data structure is used to create volcano plot from scRNA-Seq expe
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Thank you for your help! I got an error that I could not find the solution on the Internet:
library(EnhancedVolcano)
Loading required…
Comment: HTSeq error processing GFF file
by
barslmn
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1.2k
I guess you can try to replace the "?" to a "."
Also, you can copy and paste text instead of the screenshots?
Answer: DESeq2 results function runs very slow on Windows 10
by
Istvan Albert
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Note the following:
https://support.bioconductor.org/p/115415/
it looks like it has to do with the Parallel=TRUE flag
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> there is a massive difference in performance between them.
It still is taking only one minute.
Comment: HTSeq error processing GFF file
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ibq.enriquepola
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Yes,
![enter image description here][1]
[1]: /media/images/76ecd9a7-10c2-4526-9849-062605ca
Answer: How can I convert this pairwise format to fasta?
by
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This seems to be the output from `sam2pairwise` program: https://github.com/mlafave/sam2pairwise
A dirty way may be
$ grep -A 1 ^M039…
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EnhancedVolcano(CV.markers, x = "avg_log2FC", y = "p_val", lab = rownames(CV.markers),
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Actually, you get one FDR per gene if you don't loop, and perform the comparisons all at once.
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I don't have an existing tool that would do it, but if your fasta files aren't that large, it would be quite easy to do in R. You could cre…
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It's a SAM file. https://samtools.github.io/hts-specs/SAMv1.pdf
For conversion https://www.biostars.org/p/129763/
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While you're doing what @genomax says, please avoid `<pre><code>`. Use markdown (or the editor toolbar) instead.
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