Entering edit mode
6.0 years ago
jaqx008
▴
110
Hey Everyone, I am trying to map small RNAs to a genome using Bowtie1. I initially did this with the following command and with a fastq file. But this time i want to use a fasta file and don't know if the command should change or remain the same. I tried and it didn't work though. The bowtie -h is not really clear to me. Thanks
./bowtie /Users/bt1_Index /Users/Whole.clipped.fastq --un un-mapped.fastq --al mapped.fastq -S Amphioxus.male.mapped.sam
NOte: this time i am using fasta instead of fastq
In case of fastq:
bowtie [options]* <ebwt> {-1 <m1> -2 <m2> | --12 <r> | --interleaved <i> | <s>} [<hit>]
should not
-1 -2 or --12
used before /Users/Whole.clipped.fastqIn case of fasta:
If it did not work, what was the error?
Bellow is the command I just tried and it yielded a zero byte file.
I just found out that I needed to specify -f so bowtie could recognize the fasta and that worked. Thanks for your contribution
Yes I told you that in the comment above :)
Oh. My bad. I guess I just read the body of the message. Thanks again