search

ZainabKamel / NGS2-Project

This project is submitted in a partial fulfillment of the requirment of CIT-659 "NGS2" course for Nile University
Other
1 stars 0 forks source link

Using Online Galaxy Tool for trimming #15

Open ZainabKamel opened 4 years ago

ZainabKamel commented 4 years ago

Before solving the trimming command issue we used galaxy online tool for trimming the data

ZainabKamel commented 4 years ago

Then after solving the command, we used it as a comparison for the trimming data we obtained using Bash

Hadeeribrahiem173 commented 4 years ago

After looking at the QC report, we tried trimming command, but we get issue and can not fix it immediately. we searched and found a trimming tool in galaxy. we get the best parameters to modify our data in the command after trying the parameters in Galaxy which are:

Adapter sequences to use Maximum mismatch count which will still allow a full match to be performed=2 How accurate the match between the two 'adapter ligated' reads must be for PE palindrome read alignment=30 How accurate the match between any adapter etc. sequence must be against a read=10 Minimum length of adapter that needs to be detected (PE specific/palindrome mode)=8

SLIDING WINDOW Number of bases to average across=4 Average quality required=15

LEADING Minimum quality required to keep a base=3

TRAILING Minimum quality required to keep a base=3

MINLEN Minimum length of reads to be kept=36

HEADCROP Number of bases to remove from the start of the read=13

CROP Number of bases to keep from the start of the read=61