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I have a transcript assembly gtf file (filename.gtf) generated by StringTie. To find the number of assembled sequences, I used the command:
cut -f9 filename.gtf | cut -d ' ' -f4 | uniq | sort -u | wc…
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Hello,
Thanks for writing such a great tool!
I encountered a minor issue just now in which the GTF file output by the "-C" option has a few concatenated lines - e.g:
`chr1 HAVANA exon 9889097…
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15 bacterial genome sequence and annotation files links is not available. When testing with my own files, I encountered an error while running featureCounts. The failure reason is that the GTF file do…
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```
Hi,
I have been using using the gt2bed perl script for conversion. Recently I came
across this.
I downloaded gtf file (refflat hg19) from ucsc table browser. When I convert
this gtf to bed, I…
-
```
Hi,
I have been using using the gt2bed perl script for conversion. Recently I came
across this.
I downloaded gtf file (refflat hg19) from ucsc table browser. When I convert
this gtf to bed, I…
-
```
Hi,
I have been using using the gt2bed perl script for conversion. Recently I came
across this.
I downloaded gtf file (refflat hg19) from ucsc table browser. When I convert
this gtf to bed, I…
-
```
Hi,
I have been using using the gt2bed perl script for conversion. Recently I came
across this.
I downloaded gtf file (refflat hg19) from ucsc table browser. When I convert
this gtf to bed, I…
-
Hi!
Below is my rmats command
rmats.py --b1 b1.txt --b2 b2.txt --gtf gencode.v44.annotation.gtf --novelSS --allow-clipping -t paired --libType fr-firststrand --readLength 76 --variable-read-leng…
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# README description
# Synopsis
The human body contains a countless variety and diversity of cell types, states, and interactions. We wish to understand these tissues and the cell types at much …
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I used cuffcompare (v 2.2.1) to compare two sets of trasnctipts.
> cuffcompare -r $ref_gtf -s $genome -o $OUT A.gtf B.gtf
But I found the row number of result XXX.tracking is less than the number of…