LSC alignment error
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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
software-error sequence Assembly pacbio • 2.2k views
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Which mapper are you using? Did you try changing the mapping parameters on the "run.cfg" file?

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

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