How to remove redundant and poor quality ESTs
1 answer
These are not online, but can be helpful.
Redundant sequences
- Check this biostars post to remove exact duplicate sequences.
- If you want to remove sequences based on similarity cutoff, you can try cd-hit-est, uclust etc.
Poor quality sequences
- If you have reads, then you can map those reads using some mapping tools such as bowtie, BWA and check if the sequence has sufficient coverage or not. Those with insufficient must be of poor quality.
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Prakki Rama
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Prakki Rama
It depends on your requirement. If suppose you want to collapse shorter sequences covering 80% of the longer sequence with 70% identity, you need to change the parameters accordingly. Look for options -aS and -c in cd-hit. I have not used EGassembler before, so I cannot comment.
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Ram
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Prakki Rama
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Prakki Rama
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