Using the Extract Genomic DNA tool in Galaxy

Question: Using the Extract Genomic DNA tool in Galaxy

2.1 years ago by

Hi everyone!

So I am trying to use the the NGS: SAMtools function in galaxy to generate consensus sequences from BAM files that I have for genomic data. I used the generate pileup from BAM dataset tool to generate a pileup and then based on this post https://www.biostars.org/p/1388/#9471 I was trying to generate a consensus sequence in FASTA format. I did the Pileup to Interval step but when I went to do the Extract Genomic DNA step the interval dataset would not show up as an option I could extract Genomic DNA from. It would be really wonderful if someone could let me know what I am doing wrong. I am quite new to this so am not very sure of how each tool works and how the issues can be fixed.

Also does anyone know of a simple way to obtain a consensus sequence from a BAM file in FASTA or FASTQ format? I know most people use SAMtools but I am not well versed with Unix or programming at all so if there is a simpler way that would be very helpful. Please let me know. Thank you!

fasta bed extract-dna galaxy bam • 930 views

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modified 2.1 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.1 years ago by samiksha.kaul23 • 0

2.1 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

For the Extract Genomic DNA issue:

The problem could be the metadata setting on the input interval file. The "datatype" should be bed or interval, but still be in BED formatting (column) orders. Add columns as needed then use Cut to rearrange. Also, the "database" will be assigned**. Note that this will not generate a consensus (assembled) sequence from your reads - the tool is retrieving the genomic sequence that overlaps with the coordinates in the input.

**If you are working with a custom reference genome, you'll need to promote it to a custom build then assign that as the database. See the third bullet under Best Practises here: https://wiki.galaxyproject.org/Support#Custom_reference_genome

For the BAM/SAM to Fastq question:

See the tool SAM to Fastq. This will output all reads in the file, as is, no assembly.

To assemble consensus reads and output as fasta:

Other tools are needed. Trinity is one option. Others can be found in the Tool Shed http://usegalaxy.org/toolshed

Hopefully that helps, Jen, Galaxy team

ADD COMMENT • link written 2.1 years ago by Jennifer Hillman Jackson ♦ 25k

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