i ,
can you please answer my question
I am trying to use shell scripting to convert sra file to bam file
I have 3 commands i am using
1) fastq-dump SRR203400.sra
2) 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
3)samtools view -b -S SRR203400.bowtieold.sam > SRR203400.bowtieold.bam
Now i am trying use shell scripting piping operation
#!/bin/bash
# generating a fastq file using fastq dump
$1=='sraip'
$2=='hg19ref'
fastq-dump sraip |bowtie -v 3 -k 2 --sam hg19ref fastqop > $3
I am getting confused on how to pipe fast-dump output to bow tie option and use it in samtools view
Thanks in advance ,
Anusha.Ch
can you please answer my question
I am trying to use shell scripting to convert sra file to bam file
I have 3 commands i am using
1) fastq-dump SRR203400.sra
2) 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
3)samtools view -b -S SRR203400.bowtieold.sam > SRR203400.bowtieold.bam
Now i am trying use shell scripting piping operation
#!/bin/bash
# generating a fastq file using fastq dump
$1=='sraip'
$2=='hg19ref'
fastq-dump sraip |bowtie -v 3 -k 2 --sam hg19ref fastqop > $3
I am getting confused on how to pipe fast-dump output to bow tie option and use it in samtools view
Thanks in advance ,
Anusha.Ch
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