Hi ,
I am writing a script to convert sam file to bam files
I wrote script like this
#!/bin/bash
for files in *.sra
do
OUT=(${files%.sra}.bam)
ref=($"/raid/references-and-indexes/hg19/bwa/hg19.fa")
fastq-dump -Z $files|bwa aln -t 4 $ref -|bwa samse $ref -| samtools view -bS -o > $OUT
done
I got the following doubts
bwa aln database.fasta short_read.fastq > aln_sa.sai
bwa samse database.fasta aln_sa.sai short_read.fastq > aln.sam
How would my script can understand that I am taking fastq dump output and giving to bwa samse . Can some body help me to improve my code and tell me where I am going wrong .
And also I want output my file to specific directory instead of current directory like this
I want all my bam files in /raid/development/anusha/python_test/fetal_brain_bam_bwa
Thanks in advance ,
Anusha.Ch
I am writing a script to convert sam file to bam files
I wrote script like this
#!/bin/bash
for files in *.sra
do
OUT=(${files%.sra}.bam)
ref=($"/raid/references-and-indexes/hg19/bwa/hg19.fa")
fastq-dump -Z $files|bwa aln -t 4 $ref -|bwa samse $ref -| samtools view -bS -o > $OUT
done
I got the following doubts
bwa aln database.fasta short_read.fastq > aln_sa.sai
bwa samse database.fasta aln_sa.sai short_read.fastq > aln.sam
How would my script can understand that I am taking fastq dump output and giving to bwa samse . Can some body help me to improve my code and tell me where I am going wrong .
And also I want output my file to specific directory instead of current directory like this
I want all my bam files in /raid/development/anusha/python_test/fetal_brain_bam_bwa
Thanks in advance ,
Anusha.Ch
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