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Question: converting fasta file into bam file
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gravatar for nosheenfaiz09
4 months ago by
nosheenfaiz090 wrote:

Hi all,

I am new in using bioconductor can anybody tell me how to convert fasta file into bam file??

can you provide me the code?

many thanks

ngs
ADD COMMENTlink modified 4 months ago • written 4 months ago by nosheenfaiz090

I think fasta format and bam format represent totally different things, one is for sequence, the other is for alignment. Could you clarify it?

ADD REPLYlink written 4 months ago by Marlin20

Thank you

yes fasta is Raw file file i have to covert fasta file into bam file so that i could align the sequences..

ADD REPLYlink written 4 months ago by nosheenfaiz090

Hi nosheenfaiz09,

You miss an essential step in your analysis: alignment. Usually reads (in fastq format) are aligned to a reference genome, the results from such an alignment are saved in bam format, which contains information about the reads and their genome-aligned coordinates. Without alignment you cannot just convert from fastq (or fasta) to bam.

There are many aligners available, if you need one from bioconductor, you can use subread.

ADD REPLYlink written 4 months ago by b.nota290
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gravatar for nosheenfaiz09
4 months ago by
nosheenfaiz090 wrote:

Dear  b.nota 

Thank you for your reply. Yes, you are right and I did alignment and saved it as bam file but now I DONT KNOW HOW TO GET COUNT MATRIX FROM THIS BAM FILE.

ADD COMMENTlink written 4 months ago by nosheenfaiz090

This isn't an 'ANSWER' but a 'Comment'. Please use the support site appropriately.

ADD REPLYlink written 4 months ago by Martin Morgan ♦♦ 20k

A BAM file is a binary alignment/map file that holds the information on the sequences from your FASTQ raw output and the coordinates of where they map to. What you need to do now is quantify how many reads map to each transcript or gene. The usual tools for that are Cufflinks or StringTie. Have a look at the different algorithms here: http://ccb.jhu.edu/software.shtml and some background here: http://www.nature.com/nprot/journal/v11/n9/full/nprot.2016.095.html

ADD REPLYlink written 4 months ago by biomiha10
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