I have a data of small RNAome from the human cell line (SOLiD colorspace reads, 35 bp tags). I am currently using their rna2map pipeline for small RNA for alignments with the reference genome. However, I would like to test few other aligners as well to compare the results. Mainly for following reasons.
1) rna2map pipeline sometimes crashes while aligning against genome (chromosome by chromosome) and therefore if i get a better choice, i want to switch over.
2) most mappers that i have ONLY READ ABOUT doesn't trim the adaptor sequence during the alignment step. For small RNA, I am not sure where the actual read ends and where the adaptor begins. And therefore i would like to get the maximum read minus adaptor in the alignment output.
3) rna2map is poorly documented.
Can somebody who knows about these programs let me know of what to use for mapping small RNA reads (actual size of fragments in the library were between 18 and 32 bp long) generated by SOLiD v2?
Any help is appreciated.
Cheers
1) rna2map pipeline sometimes crashes while aligning against genome (chromosome by chromosome) and therefore if i get a better choice, i want to switch over.
2) most mappers that i have ONLY READ ABOUT doesn't trim the adaptor sequence during the alignment step. For small RNA, I am not sure where the actual read ends and where the adaptor begins. And therefore i would like to get the maximum read minus adaptor in the alignment output.
3) rna2map is poorly documented.
Can somebody who knows about these programs let me know of what to use for mapping small RNA reads (actual size of fragments in the library were between 18 and 32 bp long) generated by SOLiD v2?
Any help is appreciated.
Cheers