How Do I Convert From Sam To Eland Format?

Question

[KCC]

How do I convert from SAM to ELAND format?

[geneart$$]

Hi KCC , was wondering if you had an opportunity to test the pyicos suggested by Vikas Bansal? I am currently trying to convert SAM to eland to use in proTRAC software. That software specifes a eland format file generated by seqmap output using pyicos. I tried using Pyicos , but the eland format I got out of pyicos had many columns , more than what was specified by the proTRAC software input file. Was wondering if you or anyone reading this blog has had any experience using this file converter or the proTRAC software and coul dsuggest any work arounds?

Answer 1

[Vikas Bansal]

I have not tried it but you can try pyicos. It says-

Convert

Converting a file from one format to another format. Currently supported format are:

experiment: Bed, Wiggle files (bed_wiggle), SAM, Eland, bedpk (Pyicos default compressed format), bedspk (Pyicos stranded compressed format)

output: Bed, Wiggle files (bed_wiggle, variable_wiggle), SAM, Eland, bedpk (Pyicos default compressed format), bedspk (Pyicos stranded compressed format)

This operation is useful if you only want to convert your data to another format. Other operations already include a convertion if you specify different experiment and output formats.

[KCC]

It looks interesting. How tested is it?

[Vikas Bansal]

Sorry, I did not get your question. What do you mean by "How tested is it"?