isovic
total number of polished and unpolished reads equal raw data
hi, i used racon to polish nanopore reads, the output file contains polished and unpolished reads, total number of polished and unpolished reads equal raw data, is it normal? for example, three reads got one consensus sequences, the number of reads should less than the number of raw data, i don't understand.
Hello,
if you have enough data, all sequences will be polished. If you run racon with -u, the output file will contain both polished and unpolished sequences.
Best regards, Robert
hi rvaser, i'm so sorry i didn't make myself clear. my command is
minimap2 -t 10 -a -x ava-ont GA20000.fasta GA20000.fasta > GA20000.sam
racon_wrapper -u -t 5 GA20000.fasta GA20000.sam GA20000.fasta > final.fasta
i used the same RNA sequences for ”sequences“ and ”target sequences“, i want to get consensus sequences, Is it right? does racon support to get consensus sequences for RNA-sequencing?
The commands look fine, but you might not get optimal results for RNA-sequencing due to alternative splicing. Your best bet is to additionally use option -f.
hi rvaser, i have another question, consensus sequences which i got from racon, are redundant.
for example:
>0524aeb0-873b-414e-87b4-805e0abc5294r LN:i:1400 RC:i:16 XC:f:1.000000
read count is 16, which reads support this read? they should include in the final results, but i want to remove these reads, because they are redundant. how can i do it?
Unfortunately, you cannot get the identifiers of sequences used for polishing of each other sequence. You could map the polished result with itself and see if any two sequences have a large global alignment.