Hello!
I am new in NGS analysis, but in my new lab i had to replace my colleague in big NGS project related to miRNA-seq. He left me bunch of fastqs and mirbase 21 fasta file with prebuilt indexes ("old" attached file). Recently, i have downloaded mirbase 22 mature sequences as fasta file, to try to map my reads to a newer version of database. I have changed Us to Ts , and used bowtie-build to build new indexes)("new" attached file(renamed for upload). But when i run bowtie on the same samples with old file and the new one i had different results - ~35% unique mappers and ~4% multimappers with old mirbase 21 file ive got from colleague and exactly the opposite - 4% unique and ~35% multimappers - with the new file. As i said, i`m new in NGS analysis and i must be missing some simple processing step or something, that inverts my mapping results. Can you please explain what am i doing wrong and maybe give some links to good practical ngs course? Thank you!
Please paste your plain text files in GitHub gists and share the link to the gists here. Asking users to download files gives them more work to do to solve your problem in the finite volunteer time they have.
Here's a guide on how to use GitHub gists: A: How to Use Biostars Part-3: Formatting Text and Using GitHub Gists