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Old 08-12-2010, 04:31 AM   #1
Alex Clop
Location: London

Join Date: Sep 2008
Posts: 15
Default Mapping 454 reads using Galaxy online.

Dear all,

We have been trying to do Mapping assemby of 454 reads using the Galaxy webbased tool ( but we are finding problems in converting from SAM format to BAM format.

Does anyone have a workflow that they could share with us specifically for 454 reads?

-As a general pipeline, we have:

1. After getting the data, we combined the .fna and the .qual files into fastq.

2. We filtered the fastq files and we tested this using several parameters.

3. We did the Lastz option within NGS mapping.

4. We used the SAM tools for filtering.

5. Then we tried to convert from SAM format to BAM format but we did not succeed from either the filtered and the non filtered input files.

-We have also implemented this pipeline with some modifications such as:

Replace the "combine fasta and qual into FASTQ" by "Fastq groomer" (for Illumina).

Use different filters on the "Generic Fastq manipulation"

Mapping with Bowtie or BWA (for Illumina) instead of LastZ, which worked ok.

We are wondering whether we are doing something wrong or whether there are bugs in relation to the processing of 454 data.

We would much appreciate any suggestions.

Thank you in advance.

Jeelan and Alex
Alex Clop is offline   Reply With Quote
Old 08-12-2010, 05:13 AM   #2
Location: Iowa City, IA

Join Date: Jul 2010
Posts: 95

I would caution you against using bowtie for 454 data. The most common errors in 454 data are insertions/deletions in homopolymeric regions, and bowtie is unable to map anything with insertions/deletions.
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