Shell Scripting

[AnushaC]

Hi Everyone ,
Can anyone can please help me with this
I am using shell script piping to from sra to bam file

My individual commands are
fastq-dump SRR203400.sra

bowtie -v 3 -k 2 --sam /raid/references-and-indexes/hg19/bowtie-indexes/hg19 /raid/development/anusha/SRR203400.fastq > /raid/development/anusha/SRR203400.bowtieold.sam

samtools view -b -S SRR203400.bowtieold.sam > SRR203400.bowtieold.bam

I started piping like this

#!/bin/bash
# generating a fastq file using fastq dump
$1=='sraip'

$2=='hg19ref'
fastq-dump sraip |bowtie -v 3 -k 2 --sam hg19ref outputoffastqdump > $3


I am really getting confused how to use next piping . because i am using fastq dump output in bow tie input and bowtie output in sam input

Thanks in advance,
Anusha.Ch

[GenoMax]

This question has been answered in another thread: http://seqanswers.com/forums/showthread.php?t=34247

Please use the thread above so there are no parallel conversations on the same topic.