Hi all,
I am using Novoalign to align 50bp illumina SE reads to a viral genome. The reads were processed with Casava 1.8, so I have a bunch of individual read files - e.g.
read001.gz
read002.gz
.
.
read036.gz
Now, is there a way I can tell Novoalign to align all of these reads in one go? (I know I could pipe it with gunzip, but I would rather not do that). I have tried to put them in a folder and point Novoalign like so:
novoalign -f Reads/ -c 6 -F ILM1.8 --**ILQ_SKIP -d reference -k -o SAM 2> reads.novoalign_logS.txt | samtools view -S -b -q 1 - | samtools sort - reads_sortedS
But that doesn't work - neither does replacing 'Reads/' with read0*.gz.
Any thoughts?
I am using Novoalign to align 50bp illumina SE reads to a viral genome. The reads were processed with Casava 1.8, so I have a bunch of individual read files - e.g.
read001.gz
read002.gz
.
.
read036.gz
Now, is there a way I can tell Novoalign to align all of these reads in one go? (I know I could pipe it with gunzip, but I would rather not do that). I have tried to put them in a folder and point Novoalign like so:
novoalign -f Reads/ -c 6 -F ILM1.8 --**ILQ_SKIP -d reference -k -o SAM 2> reads.novoalign_logS.txt | samtools view -S -b -q 1 - | samtools sort - reads_sortedS
But that doesn't work - neither does replacing 'Reads/' with read0*.gz.
Any thoughts?
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