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ZainabKamel / NGS2-Project

This project is submitted in a partial fulfillment of the requirment of CIT-659 "NGS2" course for Nile University
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Problem of overall alignment rate of our read by Hisat2 #18

Open DrHudaAbuBakr opened 4 years ago

DrHudaAbuBakr commented 4 years ago

As we use splice aware aligner "Hisat2" to align our reads based on whole genome or even with specific chromosome (15) we found that the overall alignment of all reads approximately 5% . This low alignment let us surprised for its low rate so we searched for that reason to see if we are in the right way as 1- could be contaminants from another organism, or other non-genomic contamination and / or maybe our reads are somewhat divergent from the reference genome " https://www.biostars.org/p/333062/ " , " https://www.biostars.org/p/273924/ " 2- If our reads with good quality scores, so we BLAST a good number of unmapped reads to see if BLAST can tell us what they are. " https://www.biostars.org/p/48629/ " 4- Does the type of aligner affect on the over all alignment percentage some said that BWA give more percentage in comparison to other splice and non splice aware. " https://www.biostars.org/p/339475/ "

Hadeeribrahiem173 commented 4 years ago

We tried BWA aligner and STAR in Galaxy to figured out if the alignment rates are different from that in Hisat2, but the percentages from all are nearly the same