Entering edit mode
10.3 years ago
raj.gzra
▴
30
hi everyone i have a fungal genome and i want to know that if anybody know, how to remove contaminated scaffolds from genome. if i do BLAST my genome sequences with contaminated species genome and i found hits. anybody know that, on what basis i have to remove that hits from my scaffold or i have to remove whole contaminated sequence or only some part of scaffold if it is contaminated. thank you
Did you assemble the genome by yourself? If so, then the easiest way will be to roll back a bit - remove the reads which hit contaminants and to reassemble.
no i did not assemble. i got assembled genome. do you know how to remove contaminated scaffold ?
if it's a multi-fasta file, you just cut it off from it. now, it is not really clear what sort of hits you have - i.e. what is the evidence that it is contaminated. If I were you, I would look on the synteny map (see example) to make a decision about cutting off the whole scaffold or its part.