LSC alignment error
0
0
Entering edit mode
8.8 years ago
Medhat 9.7k

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
software-error sequence Assembly pacbio • 2.1k views
ADD COMMENT
0
Entering edit mode

Which mapper are you using? Did you try changing the mapping parameters on the "run.cfg" file?

ADD REPLY
0
Entering edit mode

It is running and I updated the answer from time , thanks for trying to help

ADD REPLY

Login before adding your answer.

Traffic: 2960 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6