Can I use different aligner instead of STAR ?

[kaanokay]

Hi,

I want use other aligner called HISAT2 in order to perform aligment step. Is this problem for downstream analysis of IRFinder?

Thanks for this nice tool ! Regards,

[dg520]

Hi @kaanokay ,

IRFinder uses STAR to calculate the genome mapability during intron reference preparation. IRFinder uses STAR to map FASTQ reads to the transcriptome during the quantification stage.

If you had already built the intron reference using IRFinder, IRFinder can do the quantification stage using BAM files generated by any other aligners. Please note, the BAM input should be in a standard BAM format and it has to be sorted by name, not coordinate.

If you want to build a specific IRFinder version purely using your own aligner, you are free to tweak the source code. Keep reading if that's the way you want to go, but other than the information below, you have to be on your own.

The STAR executions involved in IRFinder are independent chunks in the source code. You can replace them with the aligner you like, with similar parameters of you new aligner to those used in STAR call. I listed below where those chunks are:

bin/util/IRFinder-BuildRefFromEnsembl: line 183-199. Change this to how your aligner prepare reference

bin/util/Mapability: line 29-35. Change this to how you use your aligner to align reads from fasta input

bin/IRFinder: line 61. Change this to where you aligner program locates. line 62. Delete it. It's a STAR-specific parameter line 204-208. Delete it. It's a STAR-specific version check. line 458-464, 475-481, 503-509 and 520-526. Change each of these chunks to how your aligner maps read to transcriptome.

After these changes, it should put you in a good shape. But you might have to do a bit further debug. As I said, sorry you're on your own in that case.

Best, Dadi

[kaanokay]

Thanks your quick reply. I will try them to integrate with HISAT2.

[dg520]

No problem