[dpryan]

anusha@cn1:/raid/development/anusha> bowtie -v 3 -k 2 --sam /raid/references-and-indexes/hg19/bowtie-indexes/hg19 /raid/development/anusha/SRR203400.fastq > samtools view -S F /raid/development/anusha/SRR203400.bowtieold.flagtrnc.sam
Extra parameter(s) specified: "F", "/raid/development/anusha/SRR203400.bowtieold.flagtrnc.sam"
Command: bowtie -v 3 -k 2 --sam -S /raid/references-and-indexes/hg19/bowtie-indexes/hg19 /raid/development/anusha/SRR203400.fastq view F /raid/development/anusha/SRR203400.bowtieold.flagtrnc.sam
anusha@cn1:/raid/development/anusha> bowtie -v 3 -k 2 --sam /raid/references-and-indexes/hg19/bowtie-indexes/hg19 /raid/development/anusha/SRR203400.fast -F /raid/development/anusha/SRR203400.bowtieold.flagtrnc.sam
Command: bowtie -v 3 -k 2 --sam /raid/references-and-indexes/hg19/bowtie-indexes/hg19 /raid/development/anusha/SRR203400.fast -F /raid/development/anusha/SRR203400.bowtieold.flagtrnc.sam
anusha@cn1:/raid/development/anusha>

I assume you mean:

bowtie -v 3 -k 2 --sam /raid/references-and-indexes/hg19/bowtie-indexes/hg19 /raid/development/anusha/SRR203400.fastq | samtools view -S -F 0x4 -o /raid/development/anusha/SRR203400.bowtieold.flagtrnc.bam -

Or something like that, which will write to a BAM file and ignore unaligned reads.

[dpryan]

Hi Everybody ,
Can anyone explain me how to look for the SNP's in IGV browser


Thanks,
Anusha.Ch

I assume you mean "look at SNPs", since it would take forever to manually look for them in the whole genome. You should be able to answer that question yourself (hint, what should a SNP look like?).

[AnushaC]

Fastq dump and finding the contiguous reads covered by at least one read

Hi Everyone ,
I have couple of questions . Can anybody explain me in detail answers

1) When u are using fast dump if u want to output to specific place where you want what option in fastq dunpl wil give this.

fastq-dump [options] [ -A ]
fastq-dump [options]
what is the accession in the option what for it used because if i gave without option A it worked. I am using shell script to automate my process i want the output to the place i wanted .
I used above shell script it worked
#!/bin/bash
# generating a fastq file using fastq dump

fastq-dump $2 $1
but while running it came like this why ?


anusha@cn1:/raid/development/anusha/python_test/shelltest> ./SRAtoBAM.sh /raid/development/anusha/python_test/shelltest/SRR203400.sra /raid/development/anusha/python_test/shelltest/SRR203400.fastq
2013-10-01T22:02:53 fastq-dump.2.1.12 err: table not found while opening manager within database module - failed to open '/raid/development/anusha/python_test/shelltest/SRR203400.fastq'
Written 16472407 spots for /raid/development/anusha/python_test/shelltest/SRR203400.sra
Written 16472407 spots total

2) what tools will give " contiguous reads covered by at least one read "


Thanks so much in advance

Thanks,
Anusha.Ch