Question: Multiple alignment for fastq files from illumina
0
gravatar for clara_theaux
12 days ago by
clara_theaux0 wrote:

Can I make a multiple alignment in Galaxy with fastq data from illumina? Clustal tool only takes fasta files... or maybe i should convert them somehow, i can't find how I already mapped mi data to reference with bowtie so i have sam/bam files, but not fasta files...

ADD COMMENTlink modified 12 days ago by Jennifer Hillman Jackson23k • written 12 days ago by clara_theaux0
0
gravatar for Jennifer Hillman Jackson
12 days ago by
United States
Jennifer Hillman Jackson23k wrote:

Hello,

Please try these tools:

  • SamToFastq Also accepts BAM input
  • FASTQ to FASTA

Hope that helps! Jen, Galaxy team

ADD COMMENTlink written 12 days ago by Jennifer Hillman Jackson23k

Ok I need to convert fastq to fasta to use Clustal so I'll try the second one. Do you know if it produces multi FASTA or a consense sequence FASTA?

ADD REPLYlink written 12 days ago by clara_theaux0

ClustalW does not produce consensus sequence, however, NGS reads can be assembled with different tools - see the group NGS: Assembly.

Tutorials that cover assembly can be found here if interested: https://galaxyproject.org/learn/

ADD REPLYlink written 12 days ago by Jennifer Hillman Jackson23k
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