Hi, I've been running bowtie1 where I've been querying a list of 20-mers in a single fasta file against the drosophila genome as my index. I've successfully been able to generate a sam file, however after converting my sam file to .bed the bed file does not contain the associated query sequence with each hit.
I used samtools to convert the .sam file to bam and bedtools to convert bam to bed. When running samtools view, each line was outputting continuously :
W::sam_parse1] empty query name
[W::sam_parse1] empty query name
[W::sam_parse1] empty query name
[W::sam_parse1] empty query name
[W::sam_parse1] empty query name
[W::sam_parse1] empty query name
[W::sam_parse1] empty query name
Does this mean bowtie 1 is failing to output the query in the sam file, since I don't see it when I search the sam file. If so, how would I be able to include my query in the output of bowtie1
Here's the code I used in each program:
bowtie test kmer_CR43193.fasta luck.sam -v 2 --threads 6 -f --sam
sudo samtools view -S -b luck.sam > luck.bam
bedtools bamtobed -i luck.bam > luck.bed
Can you show us the output of
the FBgn genes are part of my genome index, but not sure what's on the left most column.
Indeed there are no read names. I think what happened is that you needed to let
bowtie
know that your input was in fasta format but you did not do that correctly. Try this (-f
needs to be before the fasta file name) :Then show us the command output from my command again. It should be correct this time.
Let us make sure that your fasta file does have headers. Show us the output of
Its still outputting the same .sam file.
my fasta has labels for all the kmers,