Shell Scripting help ***

[AnushaC]

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

[AnushaC]

No it is not working for me . It is saying fail to build fasta index . it is coming like this


[email protected]:/raid/development/anusha/python_test/shelltest> ./SRAtoBAM.copy.sh /raid/development/anusha/python_test/shelltest/SRR203400.sra /raid/references-and-indexes/hg19/bowtie-indexes/hg19 /raid/development/anusha/python_test/shelltest/SRR203400.bam
view: invalid option -- '/'

Usage: samtools view [options] <in.bam>|<in.sam> [region1 [...]]

Options: -b output BAM
-h print header for the SAM output
-H print header only (no alignments)
-S input is SAM
-u uncompressed BAM output (force -b)
-1 fast compression (force -b)
-x output FLAG in HEX (samtools-C specific)
-X output FLAG in string (samtools-C specific)
-c print only the count of matching records
-L FILE output alignments overlapping the input BED FILE [null]
-t FILE list of reference names and lengths (force -S) [null]
-T FILE reference sequence file (force -S) [null]
-o FILE output file name [stdout]
-R FILE list of read groups to be outputted [null]
-f INT required flag, 0 for unset [0]
-F INT filtering flag, 0 for unset [0]
-q INT minimum mapping quality [0]
-l STR only output reads in library STR [null]
-r STR only output reads in read group STR [null]
-s FLOAT fraction of templates to subsample; integer part as seed [-1]
-? longer help

Notes:

1. 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.

2. SAM->BAM conversion: `samtools view -bT ref.fa in.sam.gz'.

3. BAM->SAM conversion: `samtools view in.bam'.

4. A region should be presented in one of the following formats:
`chr1', `chr2:1,000' and `chr3:1000-2,000'. When a region is
specified, the input alignment file must be an indexed BAM file.

5. Option `-u' is preferred over `-b' when the output is piped to
another samtools command.

[dpryan]

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

-t is used if you have a SAM file without a header, which isn't the case here. Also -u is mostly useful if you're then piping the output of samtools to something else that expects BAM as input. What you want is something like:

fastq-dump -Z $1 | bowtie -v 3 -k 2 --sam $2 - | samtools view -bS -o $3 -

[swbarnes2]

Forget the shell script for a moment. Can you get these commands to work by just typing them one at a time into the command line? You need to figure that out first, before you go stringing commands you don't understand into each other.

[AnushaC]

Hi swbarness ,
these commands all working meaning my fastq dump ,bow tie and samtools view all i checked on command line . now i have a pipeline for converting single sam to bam file . Now i have 8 of those kind of file each in different subdirectory and in a directory now i want to iterate over each sam file . Hope u understood what i am saying .


Thanks,
Anusha.Ch