fastq to bam

hugh_hang · 08-29-2013, 01:33 AM

Hi!
Can anyone tell me is it possible to convert a .fastq file to a .bam file? How to convert or which tool can I use?
Thanks in advance.

GenoMax · 08-29-2013, 04:00 AM

Yes it is possible to convert a fastq file to BAM but only after you use a suitable alignment tool to align it to a reference.

JackieBadger · 08-29-2013, 04:49 AM

Fastq is raw data (input)...BAM is an alignment file (output)

One is generated from the other using mapping/ de novo assembly software...One can not simply convert

hugh_hang · 08-29-2013, 04:57 AM

Quote:

Originally Posted by JackieBadger

Fastq is raw data (input)...BAM is an alignment file (output)

One is generated from the other using mapping/ de novo assembly software...One can not simply convert

thank you, could you tell me how to align or map fastq? what tool will you recommend?

GenoMax · 08-29-2013, 05:17 AM

Quote:

Originally Posted by hugh_hang

thank you, could you tell me how to align or map fastq? what tool will you recommend?

See the link I had included in my response in post #2.

bishwo · 08-29-2013, 06:26 AM

Use FastqToSam from picard tools. Then convert sam to bam using SamFormatConverter.

maubp · 08-29-2013, 06:27 AM

Quote:

Originally Posted by JackieBadger

Fastq is raw data (input)...BAM is an alignment file (output)

One is generated from the other using mapping/ de novo assembly software...One can not simply convert

Well, you can store unmapped reads in SAM/BAM, so a simple conversion at that level is possible although not what is usually meant (aligning):
http://blastedbio.blogspot.co.uk/201...ve-sambam.html

madhavi · 01-30-2015, 10:00 PM

Hi i am new to NGS analysis. I have read and tried many answers regarding converting fastq to sam through picard tools, But it dnt work out? is there any other way to do that?thank u.

hugh_hang · 01-30-2015, 11:11 PM

Quote:

Originally Posted by madhavi

Hi i am new to NGS analysis. I have read and tried many answers regarding converting fastq to sam through picard tools, But it dnt work out? is there any other way to do that?thank u.

I am afraid I don't know more than you do. I just followed them and get something undesirable.

maubp · 01-31-2015, 04:01 AM

You probable need to use a read mapping tool like BWA or Bowtie2 to align the raw FASTQ reads to a genome giving you aligned reads in SAM/BAM format.

This is not simply "converting" from FASTQ to SAM/BAM. The tools look at each FASTQ read and search the genome looking to find where it matches best in order to "align" the read to the genome.

(I am basically repeating what GenoMax said in his first reply at the start of this thread.)

kaps · 05-22-2015, 01:51 AM

Quote:

Originally Posted by bishwo

Use FastqToSam from picard tools. Then convert sam to bam using SamFormatConverter.

Hello I seen a script on this link https://code.google.com/p/fasta-to-fastq/ that converts fasta to fastq either as standalone or unix workflow.

How can use I it either as standalone or unix?

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08-29-2013, 01:33 AM	#1
hugh_hang Member Location: Hangzhou, China Join Date: Jan 2013 Posts: 28	fastq to bam Hi! Can anyone tell me is it possible to convert a .fastq file to a .bam file? How to convert or which tool can I use? Thanks in advance.

08-29-2013, 04:00 AM	#2
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,082	Yes it is possible to convert a fastq file to BAM but only after you use a suitable alignment tool to align it to a reference.

08-29-2013, 04:49 AM	#3
JackieBadger Senior Member Location: Halifax, Nova Scotia Join Date: Mar 2009 Posts: 381	Fastq is raw data (input)...BAM is an alignment file (output) One is generated from the other using mapping/ de novo assembly software...One can not simply convert

08-29-2013, 06:26 AM	#6
bishwo Junior Member Location: Finland Join Date: Jan 2012 Posts: 8	Use FastqToSam from picard tools. Then convert sam to bam using SamFormatConverter.

01-30-2015, 10:00 PM	#8
madhavi Member Location: India Join Date: Jan 2015 Posts: 14	Hi i am new to NGS analysis. I have read and tried many answers regarding converting fastq to sam through picard tools, But it dnt work out? is there any other way to do that?thank u.

01-31-2015, 04:01 AM	#10
maubp Peter (Biopython etc) Location: Dundee, Scotland, UK Join Date: Jul 2009 Posts: 1,543	You probable need to use a read mapping tool like BWA or Bowtie2 to align the raw FASTQ reads to a genome giving you aligned reads in SAM/BAM format. This is not simply "converting" from FASTQ to SAM/BAM. The tools look at each FASTQ read and search the genome looking to find where it matches best in order to "align" the read to the genome. (I am basically repeating what GenoMax said in his first reply at the start of this thread.)