mapping of reference file

Question

[Bulbul Ahmed]

I have finished de novo assembly, I got a reference.fasta file. Now I have to go for mapping. please suggest me how to do with bowtie 2? If there is any intermediate job require in between then also please support.

[Pierre Lindenbaum]

what have you tried?

[Bulbul Ahmed]

I have assembled the data through trinity sir...

Answer 1

[swbarnes2]

A fasta file is suitable for alignment with bowtie 2, of course you must use bowtie's indexer to make an index of that file before aligning. You will get far more helpful answers here if you say what you tried, and why you think it failed, and paste what exactly you did, rather than asking for generic "help" with no evidence of having even tried yourself.

[Bulbul Ahmed]

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

this is the command I used for mapping. but it generating a blank file

[swbarnes2]

Did it return any errors? What command line did you use to make the index?

You have to figure that people here will be willing to put in a fraction of the time helping that you show you spent trying on your own. Do you think that your posts make someone think that you tried for a solid 10 minutes? For example, how much time did you take to make sure that your command line really is put together correctly?

[Bulbul Ahmed]

I do not care sir what people do... just I know good peoples will help me. so, I post it......n I am sure they will answer me.. sir...