NGS-Ig data

[pablo12]

Dear users,

I'd like to ask you for your advise on a certain project that I am working on.

My job is to retrospectively analyse NGS data from patients suffering from ALL and MM (IGH).
However, I am not a bioinformatician. I just received the sequencing data in Excel (and .csv) files and I'm supposed to analyse these data.

Of course, I've heard of IMGT/VQUEST and IgBlast and it is no problem for me to work with these programmes. But the issue is that I can't do this with tens of thousands of sequences.

After further research, I came across the R tool tcR. It seems to be a well-done programme. Unfortunately, I always receive error messages when trying to integrate my files in it.

I found out that it might be useful to convert my files into .txt files or to work with VDJ-tools, Immunoseq, mixcr or other tools. But I do not have access to these programmes or they require Linux (which I don't have; Windows).

In addition, the sequencing data in my Excel files are not in fasta-format. But if I would change this by editing the sequences manually I'd be busy for the next three months.

My goal is to analyse my data for gene usage and to be able to search quickly for potential subclones.


I look forward to hearing your opinion!
Thanks in advance!

Pablo

[colindaven]

You can probably use the sequences from the CSV files to create fasta files with a bit of creativity.

Have a look at good text editors like Notepad++ to get this done.

Also check out Galaxy for user friendly processing tools.