I keep getting error messages when submitting HTSeq jobs, using both -
(a) sorted (by chromosomal coordinates) and
(b) unsorted bam files
I made sure to specify the appropriate order in the HTSeq options: "-r pos" for both sorted and unsorted. I'm re-running samtools now to sort by name, but I'm not sure that's necessary (since you can specify position in the order option.)
Here is the error message I get when specifiying the unsorted bam file:
Error occured when processing SAM input (record #1794713 in file /xx/xx_Aligned.out.bam I am not sure why it's referring to a sam input. Am I better off converting to sam? Is there anything else I could be missing
And here is the error message I get when specifying the sorted bam file:
Error occured when processing GFF file (line 1611183 of file /xx/GTF/Homo_sapiens.GRCh37.65.gtf)
I'm sure this is a common problem and that there are many posts about this. I am certainly looking into it but in the meantime was hoping to get any feedback if you're familiar with this. Clearly I'm a newbie to this kind of analysis.
Thank you so much!