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How to get a bam file
28-Apr-2015, 08:54 AM
Post: #1
How to get a bam file
The query below concerns how to get a bam file of the alignments in RiboGalaxy and related questions:

Hi
I have one question, I generated the coverage and ribosome profile for my samples an scan view in Gwips.
I need to know how I can get a bam file for these.
And also how do I convert them into a txt/excel file with read count value for each gene/transcript.
I will need to normalize it with total RNA read count.
Please advice. Thanks
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28-Apr-2015, 08:55 AM
Post: #2
RE: How to get a bam file
Hi,

If you have used one of the GWIPS-viz workflows (available as Published Workflows under the Shared Data tab), then a BAM file of the alignments to the genome should have been generated for the alignment output. Alternatively, if you align to a transcriptome using bowtie in the Transcriptome Mapping suite, a SAM file will be generated. The SAM file can be converted to BAM using the option under the Convert Formats tools. These files can be downloaded for further analysis.

Unfortunately we do not yet provide a tool to extract gene/transcript read count values. However, this is an excellent suggestion and we plan to provide such a tool shortly. We also plan to add a tool for differential gene expression analysis that takes into account the mRNA-seq read count.

Thanks for your interest in RiboGalaxy and if you have any further questions, please post to the Forum and we will try our best to address your query.

Kind Regards,
The RiboGalaxy Team
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13-Apr-2017, 08:30 AM
Post: #3
RE: How to get a bam file
My question is about the sam-to-bam conversion.

What is the purpose of selecting the reference dataset? When I selected the whole genome as the reference, it wouldn't convert my files, but when I selected the rRNA sequence file I used for subtraction, it converted fine. I don't really understand why the reference genome file is needed when it's just converting one sam file (that doesn't contain the rRNA reference sequences anyway because I've already subtracted them) into a different format. This makes me think I don't really understand what's going on here, and I'd like to! Please could somebody explain? Thanks!
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18-Apr-2017, 09:18 AM
Post: #4
RE: How to get a bam file
Hi there,

The conversion of the sam file to bam format requires the reference sequences FASTA (genome or transcriptome) to which the reads were mapped.

We are perplexed as to why the rRNA sequences FASTA worked in this instance if the sam output was from the alignment to other sequences.

When it is convenient, could you contact the RiboGalaxy team by email with details of the data history so that we can troubleshoot more on this issue.

Kind regards,
Audrey
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19-Apr-2017, 07:17 AM
Post: #5
RE: How to get a bam file
Dear Audrey,

Thanks so much for your reply.

Please could you tell me which email address to use to send this info and which (if any) files I should send?

Best wishes,

Beth
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21-Apr-2017, 09:45 AM
Post: #6
RE: How to get a bam file
Hello,
sorry about the delay in answering. You could send the details to RiboGalaxy@gmail.com.
Let us know where the files are in your RiboGalaxy account i.e. name of history and id/name of the dataset in your history like example below:

12: human_sample_CTGTAGGCACCATCA.fastq

This should avoid having to send the files by email.

Kind Regards
jamesp

The RiboGalaxy Team
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