No successful assigned alignments using featureCounts

[James D. Lauderdale]

I am having problems generating a count matrix using featureCounts (Rsubread package). Attached is a screen shot of the output. Here GTF.attrType is set for "transcript_id" but same results are obtained  if set to "gene_id". The BAM files contain alignments from the previous step. I am guessing that the problem is with the GTF file that I am using: link to file: https://drive.google.com/drive/folders/1moN-skNc23p-YSysA6MF_0eX9LGr00cQ?usp=sharing

Any and all assistance most appreciated. Thanks, Jim

[Yang LIAO]

Hi James,

I took a look at the GTF file and BAM file, and they used very different sequence names.

The GTF file uses sequence names like "scaffold_2386", while the BAM file uses sequence names like "ANOSAGT000769(LUZP2)". You need to find the map between the two types of sequence names or featureCounts cannot find the annotations in the GTF file on the same sequence of the read. When you have the map between the sequence names, you can give it to featureCounts in the "chrAliases" option.

Cheers,

Yang