how to use bowtie-inspect

Question

[mra8187]

Dear all how can i use bowtie-inspect .. my script is :

bowtie-inspect -s indexed-refrence.fa | tail -n +4 | cut -f 2- > '/home /mra/Desktop/genome_size.txt' | cat junctions.bed | bed_to_juncs | flankBed -g '/home/mra/Desktop/genome_size.txt' -b 1 | slopBed -g '/home/mra/Desktop/genome_size.txt' -b 2 > '/home/mra/Desktop/windows.bed'

an i get this error :

cat: junctions.bed: No such file or directory Could not locate a Bowtie index corresponding to basename "indexed-refrence.fa" Command: bowtie-inspect --wrapper basic-0 -s indexed-refrence.fa

[Joe]

Well the error is telling you that file doesn't exist...so maybe start there? You need to tell us what you're trying to do. When you're trying to build complex pipes like that, build them step by step so that you can be sure that the outputs and inputs you're getting are what you expect.

[mra8187]

thank you for your answer. i try to snp discovery by :

samtools mpileup -u -q 10 -f reference.fa accepted_hits.bam | bcftools view -g - | vcfutils.pl varFilter | awk '($6 >= 50)' > holstein.raw.pileup

and i get snp list .. then i trying to filtering snp by this :

Filter SNPs by Bedtools

./bowtie-inspect -s reference.fa | tail -n +4 | cut -f 2- > genome_size.txt cat junctions.bed | python2 bed_to_juncs | ./flankBed -g genome_size.txt -b 1 | s./lopBed -g genome_size.txt -b 2 > windows.bed ./intersectBed -v -wa -a holstein.raw.pileup -b windows.bed > holstein.filtered.pileup

it is wrong ?

can you help me to filtering snp by another script an another packages ?

[GenoMax]

I made a minimal change to the title of this post to make it semi-legible.

This post can use additional information about what you are trying to do besides a correction to the title.