Entering edit mode
9.4 years ago
Medhat
9.8k
I am trying to use LSC which correct PacBio reads ;
One of the sections in the run.cfg
file contains these information
##
# Remove PacBio tails sub reads? (Y or N)
# The names of PacBio long reads must be in the format of the following example: ">m111006_202713_42141_c100202382555500000315044810141104_s1_p0/16/3441_3479"
# The last two numbers (3441 and 3479 in this example) are the positions of the sub reads.
# (single value)
I_RemoveBothTails = Y
but my read is just somename.fastq
I run the program and it give me this error
===split LR_SR.map:===
Error: No short reads was aligned to long read. LSC could not correct any long read sequence.
Shall I change the pacbio read name or what shall I do any idea? and If I need to change the name how shall it be changed?
UPDATE:
change
I_RemoveBothTails = N
Which mapper are you using? Did you try changing the mapping parameters on the "run.cfg" file?
It is running and I updated the answer from time , thanks for trying to help