Hello, i am a new Velvet user and i am trying to assemble some libraries that i found in this site:
I have some question about Velvet:
1) Shuffle operation is needed always when more than 1 library is assembled? If is not needed always in what it helps?
2)I saw this operation in the recipes of the site i mentioned:
shuffleSequences_fastq.pl shortjump_1.fastq shortjump_2.fastq - | fastx_reverse_complement > shortjump.fastq
What - | fastx_reverse_complement > shortjump.fastq is needed for?
3)Using the the command above i have the following error:
/var/spool/slurmd/job414800/slurm_script: line 21: fastx_reverse_complement: command not found
Why this error is produced? Is it a problem of slurm? Can i fix it or there is another alternative?
4) I also tried to use:
fastq -shortPaired frag.fastq -shortPaired2 shortjump.fastq -shortPaired3 longjump.fastq
but i have a problem with -shortPaired3. I have to put at max 2 parameters?
Thank you a lot
I have some question about Velvet:
1) Shuffle operation is needed always when more than 1 library is assembled? If is not needed always in what it helps?
2)I saw this operation in the recipes of the site i mentioned:
shuffleSequences_fastq.pl shortjump_1.fastq shortjump_2.fastq - | fastx_reverse_complement > shortjump.fastq
What - | fastx_reverse_complement > shortjump.fastq is needed for?
3)Using the the command above i have the following error:
/var/spool/slurmd/job414800/slurm_script: line 21: fastx_reverse_complement: command not found
Why this error is produced? Is it a problem of slurm? Can i fix it or there is another alternative?
4) I also tried to use:
fastq -shortPaired frag.fastq -shortPaired2 shortjump.fastq -shortPaired3 longjump.fastq
but i have a problem with -shortPaired3. I have to put at max 2 parameters?
Thank you a lot
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