bioinformatics command line

Question

[Bulbul Ahmed]

May I get the commands for bowtie2 in pbs script for mapping assembled data. kindly give me it in < Email address removed >

My de novo assembly file is in fast format. so it need to convert into sam format. what should be the command for converting fasta format into sam file. I used

bowtie --best --strata -m1 --sam -l 36 -n 3 h_sapiens_ncbi36 -q assembly.fasta > SAMPLE.sam

but this command show error. only a blank .sh file generated

[Devon Ryan]

How about you post what you've tried rather than asking us to do everything for you.

[Bulbul Ahmed]

I have have tried but I could understood the command that provided in bowtie manual.

[Devon Ryan]

Then ask for clarification on the parts you didn't understand. You also don't need all of the options, just -x and either -U or -1 and -2.

[Bulbul Ahmed]

[bowtie2 -p16 -x <path of the bowtie2> -1 dat_1.fastq -2 data _2.fastq -s <path of the reference> reference.fasta ]

The above command I used but its working in pbs script. so please help me out to work it in bs script

[Devon Ryan]

I assume you mean:

bowtie2 -p 16 -x <path of the bowtie2> -1 dat_1.fastq -2 data_2.fastq -S something.sam

When something doesn't work, you need to provide further information about what that means. We don't read minds.

[Bulbul Ahmed]

so I have to convert the reference.fasta file into SAM format???

[Devon Ryan]

No, you don't fasta file isn't used after the index is built.

[Bulbul Ahmed]

then what shall I do??

[Michael]

You want to align assembled contigs to the genome, as I wrote earlier this is an XY problem: you want to do X (align contigs to genome) you think that Y (running bowtie in PBS) is a solution to X, so you ask how to use bowtie with PBS to align fasta files. But bowtie is not a solution to aligning contigs to the genome.

[andrew.j.skelton73]

http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml

[Bulbul Ahmed]

please also send all the commands related to this problem till path analysis of gene. actually i am working in server by using pbs script.

[Michael]

Hello ahmedbulbul52!

We believe that this post does not fit the main topic of this site.

I guess that you want to submit a bowtie job to the PBS cluster using qsub? If so, you need to read man qsub and give more context than a single sentence. Devoid of context, this question cannot be answered, therefore it has to stay closed until further information is given. Also, please don't take the discussion to personal email, note I deleted your email address.

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

[Bulbul Ahmed]

sir my de novo assembly file is in fast format. so it need to convert into sam format. what should be the command for converting fasta format into sam file. I used bowtie --best --strata -m1 --sam -l 36 -n 3 h_sapiens_ncbi36 -q assembly.fasta > SAMPLE.sam. but this command show error. a blank file is generating

[Michael]

Thanks for the update, you may edit your question directly next time. I have re-opened it, but there is still many things that are confusing:

my de novo assembly file is in fast format

where does that file come from? which length of contigs did you get, and how many are they from human sequences? Are they RNA/DNA?

so it need to convert into sam format

why?

I used bowtie... h_sapiens_ncbi36

why would you use bowtie to align contigs to the genome? Bowtie is a short read aligner, you should use something else to align a assembled contigs? Why do you align against an old asembly ncbi36?

but this command show error

what is the error message (or is there no error message)

So I guess this is an XY problem: http://meta.stackexchange.com/questions/66377/what-is-the-xy-problem

[Bulbul Ahmed]

Sir after de novo assembly, I got a reference.fasta file.Now I have to go for mapping. Before that I need to convert this .fasta into .sam format. These are the DNA and the datas are from buffalo. Now kindly tell me how will I will convert this file into a .bam file using bowtie 2. Please tell me the command we use

[Michael]

I still think you shouldn't use bowtie for this, instead you should use something like Mauve, Contiguator, bwa mem, MUmmer.

[seta]

This is an example of PBS file:

#!/bin/bash
#PBS -N (write the name of your job)
#PBS -l nodes=1:ppn=6 (specify the required thread)
#PBS -l walltime=250:00:00 (specify the required time to finish the job)
#PBS -l mem=80gb (write the required memory)
#PBS -o stdout_file
#PBS -e stderr_file

#then write your executable command, for example
bowtie2 -p 16 -x <path of the bowtie2> -1 dat_1.fastq -2 data_2.fastq -S something.sam (as Devon suggested).

Finally save this file as text file, say run_1.sh and submit to server using qsub run_1.sh

Hope this helps

[Bulbul Ahmed]

sir I have the pbs script. my de novo assembly file is in fast format. so it need to convert into sam format. what should be the command for converting fasta format into sam file. I used

bowtie --best --strata -m1 --sam -l 36 -n 3 h_sapiens_ncbi36 -q assembly.fasta > SAMPLE.sam

but this command show error. only a blank .sh file generated

[Bulbul Ahmed]

Sir after de novo assembly, I got a reference.fasta file.Now I have to go for mapping. Before that I need to convert this .fasta into .sam format. These are the DNA and the datas are from buffalo. Now kindly tell me how will I will convert this file into a .bam file using bowtie 2. Please tell me the command we use

Answer 1

[Michael]

So you have a FASTA file and are supposed to use -f but you used -q. This will not work, apart from that you are most likely trying to do the wrong thing. And what is more, you are seemingly confusing bowtie 1 and bowtie2 as to your comments.

From the bowtie manual which you are supposed to read.

-q The query input files (specified either as <m1> and <m2>, or as <s>) are FASTQ files (usually having extension .fq or .fastq). This is the default. See also: --solexa-quals and --integer-quals.

-f The query input files (specified either as <m1> and <m2>, or as <s>) are FASTA files (usually having extension .fa, .mfa, .fna or similar). All quality values are assumed to be 40 on the Phred quality scale.