I have a total RNAseq dataset that I aligned using STAR producing BAM files (sorted by coordinates). I am now trying to get counts for the lncRNA sequences using htseq-count, with the command:
htseq-count -m intersection-nonempty -f bam -i gene_id -r pos -s reverse ./OVCA429_Aligned.sortedByCoord.out.bam ./GRCh38_latest_genomic.gtf > ./OVCA429.counts.txt
This is the output:
[E::idx_find_and_load] Could not retrieve index file for './OVCA429_587680_1_1.rnaseq.fastqAligned.sortedByCoord.out.bam'
100000 GFF lines processed.
200000 GFF lines processed.
300000 GFF lines processed.
400000 GFF lines processed.
...(truncated output here)...
3775001 GFF lines processed.
[E::idx_find_and_load] Could not retrieve index file for './OVCA429_587680_1_1.rnaseq.fastqAligned.sortedByCoord.out.bam'
100000 alignment records processed.
200000 alignment records processed.
300000 alignment records processed.
...(truncated output here)...
Output text file:
__no_feature 20368875
__ambiguous 0
__too_low_aQual 0
__not_aligned 0
__alignment_not_unique 2634439
I've read through the htseq-count literature but it never asks to include an index file, therefore i'm not sure how to deal with this problem. Any help/ suggestions would be welcome! Thank you, in advance.