Geo Chip-Seq Data To Sam File

Question

[darcangelo.elisa]

Hi everyone,

I need to transform NCBI GEO ChIP-seq data to sam file. Specifically, the data (GSE28352_RAW.tar) available at the very bottom of this page: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE28352 I am having problems using samtools for this conversion, I don't know if the problem lies within the files or samtools.

Every help will be greatly appreciated,

Thank you!!

elisa

Answer 1

[Istvan Albert]

A SAM file is a Sequence Alignment/Map format that describes the alignment of each read relative to a target (reference) data.

A quick look at the data sets makes me think these are in the so called ELAND format - a nonstandard way earlier Illumina machines have outputted the data. For that you may want to look at:

http://www.biostars.org/post/show/3121/how-to-convert-eland-file-to-bam/

In all you will probably need to reformat this file, to contain 11 columns as per the SAM specification. But even after you do so be advised that there may be attributes that cannot be recovered from this file.

Answer 2

[darcangelo.elisa]

That helps a lot, thank you so much!! :)

elisa