Hello all, I am trying to switch over to using hisat2 instead of tophat. I have a couple questions:
1. It seems that we are able to input a list of mates for -1 & -2. Would this be referring to inputing multiple paired reads of the same sample in to be aligned at once? For example I have 8 .fastq files (4 paired reads) - how would the input look like?
2. How do I create a specific output file and directory? Would this be using the -S flag and inputing a file name after that? I see that the default output is .sam, is there a way to output .bam files?
3. I tried to use the multithread option, -p/--threads 4, (as I have 4 cores) but got this error: -p/--threads arg must be at least 1. Any help with this?
1. It seems that we are able to input a list of mates for -1 & -2. Would this be referring to inputing multiple paired reads of the same sample in to be aligned at once? For example I have 8 .fastq files (4 paired reads) - how would the input look like?
2. How do I create a specific output file and directory? Would this be using the -S flag and inputing a file name after that? I see that the default output is .sam, is there a way to output .bam files?
3. I tried to use the multithread option, -p/--threads 4, (as I have 4 cores) but got this error: -p/--threads arg must be at least 1. Any help with this?
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