Fastq to Sam

[madhavi]

Hii everyone i have read about conversion of Fastq to sam through picard tools and alignment with bowtie(which directly gives sam output) both dnt worked out with my fastq files ? please suggest any other way? thanks in advance

[dpryan]

You're unlikely to want to convert your fastq files to SAM format. Why don't you tell us what went wrong with the bowtie alignments?

[madhavi]

Bowtie error

Hii
I tried to reinstall bowtie2, it is showing an error 'bin/sh: 1: clang++: not found
make: *** [bowtie2-build-s] Error 127'
help me to solve this thank u

[dpryan]

Either install the clang compiler or, more simply, just download the binary for bowtie2 so you don't even need to compile things.

[madhavi]

Hii dpryan
Thanks i could successfully install and run bowtie2 to some extend. but after creating the reference index file and when i was trying to align reads it is showing an error like
Extra parameter(s) specified: "reads1.fq", "lambda.sam"
Error: Encountered internal Bowtie 2 exception (#1)
bowtie2-align exited with value 1
any one please suggest how to sort this.

[dpryan]

You likely typed the command incorrectly. We'd need to know the exact command you typed to help.

[madhavi]

the command i used is
bowtie2-2.2.4$ bowtie2 -p 12 -N 1 -t -x /bt2-index/yeast_index -1 testR1.fastq -2 testR2.fastq -S test.sam

[dpryan]

That command couldn't have produced the error message you posted. Don't modify the command you posted, copy and paste the exact command that produced the error.

[madhavi]

NGSprograms/bowtie2-2.2.4$ bowtie2 -p 12 -N 1 -t -x /NGSprograms/bowtie2_2.2.4/bt2-index/yeast_index -1 yeastR1.fastq, -2 yeastR2.fastq -S yeast.sam

[Nathan765]

NGSprograms/bowtie2-2.2.4$ bowtie2 -p 12 -N 1 -t -x /NGSprograms/bowtie2_2.2.4/bt2-index/yeast_index -1 yeastR1.fastq, -2 yeastR2.fastq -S yeast.sam

Hi, you've got a comma after yeastR1fastq. Could be the problem?

[madhavi]

Hii
i am ruuning samtools to create variation report by using the following commond it showed an error Segmentation fault (core dumped)
how to solve this ?
NGSprograms/samtools-1.2$ samtools mpileup -g -f ChrAll.fasta bpt1.sorted.bam.bam > bpt.bcf

[dpryan]

Check to see if "ChrAll.fasta" and "bpt1.sorted.bam.bam" exist.