Shell Scripting help ***

[AnushaC]

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

[rhinoceros]

#!/bin/bash
# generating a fastq file using fastq dump
sraip=$1
hg19ref=$2
fastq-dump $sraip | bowtie -v 3 -k 2 --sam $hg19ref fastqop > outputfile

or alternatively

#!/bin/bash
# generating a fastq file using fastq dump
fastq-dump $1 | bowtie -v 3 -k 2 --sam $2 fastqop > outputfile

Now you would call your script "script.sh /where/ever/it/is/sraip.file /where/ever/it/is/hg19reffile". Don't know if it works. I'm just demonstrating how you hadn't quite grasped how to use variables. In shell scripts $1 is the first thing after the program name when calling the script, $2 the second, etc. Variables are assigned as variableA="something" and then referred to by $variableA, e.g.

variableA="Hello"
echo $variableA

[dpryan]

@rhinoceros, yeah, that won't do what you want.

fastq-dump -Z $1 | bowtie -v 3 -k 2 --sam $2 - $3

where $3 is an output name. You need to use the -Z flag so fastq-dump doesn't write instead to a file and pass - as the input file name to bowtie so it knows to read from stdin. In a real script, you'd have the output name generated according to the name of the SRA file. Also, piping input into bowtie won't work for paired-end data (not to mention that you should always QC SRA data prior to alignment as a lot of it is low quality).

[AnushaC]

shell Scripting ***

Hi ,
I need to pipe third program which is samtools view to make sam to bam


fastq-dump -Z $1 | bowtie -v 3 -k 2 --sam $2 - |samtools view -b -S > $3

what will direct my output to sam tools view.


Thanks in advance ,
Anusha.Ch

[dpryan]

fastq-dump -Z $1 | bowtie -v 3 -k 2 --sam $2 - |samtools view -b -S > $3

That's almost correct. Have a look at the samtools manual for what you're missing (hint, it's a -).

[AnushaC]

Hi ,
You guys talking about only two of my outputs but i have three program i am using samtools view to convert sam file to bam file . I am trying but will direct sam to bam output with piping

Thanks,
Anusha.Ch

[dpryan]

You guys talking about only two of my outputs but i have three program i am using samtools view to convert sam file to bam file.

I'm aware that you're trying to then convert to a BAM file by piping to samtools. Please actually read my reply and then do what I wrote. I could simply write the full command, but then you'd not start to learn how to properly create these commands yourself.

[AnushaC]

Hi Ryan,
That is not correct . I am getting error


Thanks,
Anusha.Ch

[dpryan]

That is not correct . I am getting error

Whatever you're typing may be incorrect, but what I told you to do is not (btw, when you receive an error message, it's usually best to actually post it).

[AnushaC]

Hi Ryan ,



fastq-dump -Z $1 | bowtie -v 3 -k 2 --sam $2 -|samtools view -u -t -F 4 -$3

will this work do i need to use faidix also

Thanks,
Anusha.Ch

[dpryan]

fastq-dump -Z $1 | bowtie -v 3 -k 2 --sam $2 -|samtools view -u -t -F 4 -$3

Again, the samtools command isn't specified correctly. Reread the samtools manual (and why are you using -t?).

[AnushaC]

Hi Ryan,
I read the manual and If `-t' is
applied, the input file is assumed to be in the SAM format. so i started using -t but it did not work for -t or -T i did try by giving reference file . I did not understand where i am going wrong .

Thanks,
Anusha.Ch

[dpryan]

That's not what the manual says regarding -t.

[AnushaC]

By default, this command assumes the file on the command line is in
the BAM format and it prints the alignments in SAM. If `-t' is
applied, the input file is assumed to be in the SAM format. The
file supplied with `-t' is SPACE/TAB delimited with the first two
fields of each line consisting of the reference name and the
corresponding sequence length. The `.fai' file generated by `faidx'
can be used here. This file may be empty if reads are unaligned.

this what i got when i trying to run command then i changed to like this


#!/bin/bash
# generating a fastq file using fastq dump
sraip=$1
hg19ref=$2
fastq-dump -Z $1 | bowtie -v 3 -k 2 --sam $2 -|samtools view -u -S -$3

It also did not work ,then i tried giving samtools view -u -T $2 -$3 and
samtools view -u -t $2 -$3 none of this worked

[AnushaC]

Hi ,


fastq-dump -Z $1 | bowtie -v 3 -k 2 --sam $2 -|samtools $2 -| samtools view -u -t -$3

will this work ?

Thanks,
Anusha.Ch