pseudoalignments.bam to bed file?

[dtomas1989]

Hi all, I am using kallisto with this command:

kallisto quant -i kallisto_index --bias --genomebam --chromosomes chrm.sizes.txt --gtf ITAG3.10_gene_models.gtf -o test R2_001.tr.fq.gz R2_001.tr.fq.gz

But now I want convert my bam file from kallisto to a bed file but i have the following mistake:

bedtools bamtobed -i pseudoalignments.bam

Error: terminate called after throwing an instance of 'std::out_of_range' what(): vector::_M_range_check: __n (which is 18446744073709551615) >= this->size() (which is 13) Any suggestions?, thanks in advance

[Rhinogradentia]

I had kind of a similar problem which was solved by using another gtf. The main problem was the gtf format. The error message seems to has something to do with coordinates or sequence lenghts I would suggest. Maybe the information to the gtf file format in this thread helps: https://github.com/pachterlab/kallisto/issues/155