Error in seq.default(start, max(start + 1, end - 4), by = 2425)

[archana433]

$ ./sashimi-plot.py -b input_bam.tsv -g nochr_gencode_exon_transcript.gtf -c 2:29,619,720-29,740,978 -M 10 --base-size=20 --ann-height=4 --height=3 --width=18 -P palette.txt

Error in seq.default(start, max(start + 1, end - 4), by = 2425) :
'from' must be of length 1
Calls: rbind -> [ -> [.data.table -> seq -> seq.default
Execution halted

[dgarrimar]

I think you should remove the commas for the region: 2:29619720-29740978

[archana433]

nochr_gencode_full (copy).zip
i attached the gtf file also
$ ./sashimi-plot.py -b input_bam.tsv -g nochr_gencode_exon_transcript.gtf -c 2:29619720-29740978 -M 10 --base-size=20 --ann-height=4 --height=3 --width=18 -P palette.txt

Error in seq.default(start, max(start + 1, end - 4), by = 2425) :
'from' must be of length 1
Calls: rbind -> [ -> [.data.table -> seq -> seq.default
Execution halted

[dgarrimar]

Could you try only ./sashimi-plot.py -b input_bam.tsv -g nochr_gencode_exon_transcript.gtf -c 2:29619720-29740978?, also with and w/o the annotation file to get some hint on the source of the problem. Can you reproduce our examples? In any case, could you provide some sample data to try to reproduce the error? Thanks!

[archana433]

$ ./sashimi-plot.py -b input_bam.tsv -g nochr_gencode_exon_transcript.gtf -c 2:29619720-29740978
Error in seq.default(start, max(start + 1, end - 4), by = 2425) :
'from' must be of length 1
Calls: rbind -> [ -> [.data.table -> seq -> seq.default
Execution halted

and when i am trying without gtf it is working.

[dgarrimar]

So the problem could be the annotation. I see you use nochr_gencode_exon_transcript.gtf. Could you try using the full annotation? Still, it would be really useful that you provide some example data in which we can reproduce the error. It can be just a (downsampled) bam file.

[dgarrimar]

Hi @archana433, did you manage to resolve the problem?

[archana433]

yes, it is solved , Thank you

[archana433]

I am getting this error again and also attaching the example data.
./sashimi-plot.py -b example1.bam -c 2:29619720-29740978 -g encode_mm10.transcript.exon.gtf
Error in seq.default(start, max(start + 1, end - 4), by = 2425) :
'from' must be of length 1
Calls: rbind -> [ -> [.data.table -> seq -> seq.default
Execution halted

gencode_mm10.transcript.exon.zip

example1.zip

[dgarrimar]

It seems that when there is only one intron of length shorter or equal to 5bp annotated in one of the strands (in your case the only intron annotated for transcript ENSMUST00000051212.3), an error arises in the arrow drawing due to an empty object. It should be fixed now.