hisat2 -x mm9_index/mm9 SRR443883_1.fastq.gz --reorder -S SRR443883_1.sam.gz
Without -U in front of the zipped fastq, than you get:
Error: reads file does not look like a FASTQ file terminate called after throwing an instance of 'int'
If you use -U it works as it should. However, if you use an uncompressed fastq file it works with -U and without it.
I think hisat2 should behave the same for compressed and uncompressed files.
Hello,
if you run:
hisat2 -x mm9_index/mm9 SRR443883_1.fastq.gz --reorder -S SRR443883_1.sam.gzWithout-Uin front of the zipped fastq, than you get:Error: reads file does not look like a FASTQ file terminate called after throwing an instance of 'int'If you use
-Uit works as it should. However, if you use an uncompressed fastq file it works with-Uand without it. I think hisat2 should behave the same for compressed and uncompressed files.