Error Running leafcutter_cluster_regtools.py

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Jan 31, 2021, 3:09:42 PM1/31/21

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Hello ,

Can you please help me ? I ran the following code, and got the error message which I do not understand.

Thank you.

python /kuacc/users/akashgari19/apps/leafcutter/scripts/leafcutter_cluster_regtools.py -j test_juncfiles.txt -m 50 -o testYRIvsEU -l 500000

scanning /kuacc/users/akashgari19/CutterLeaf_STAR_Mapping/con2_mapping/CON-2Aligned.sortedByCoord.out.bam.junc...

Parsing...

X:+..17:+..17:-..9:?..16:-..1:?..Y:-..18:+..19:?..Traceback (most recent call last):

File "/kuacc/users/akashgari19/apps/leafcutter/scripts/leafcutter_cluster_regtools.py", line 497, in <module>

main(options, libl)

File "/kuacc/users/akashgari19/apps/leafcutter/scripts/leafcutter_cluster_regtools.py", line 14, in main

pool_junc_reads(libl, options)

File "/kuacc/users/akashgari19/apps/leafcutter/scripts/leafcutter_cluster_regtools.py", line 68, in pool_junc_reads

clu = cluster_intervals(read_ks)[0]

File "/kuacc/users/akashgari19/apps/leafcutter/scripts/leafcutter_cluster_regtools.py", line 316, in cluster_intervals

current = E[0]

IndexError: list index out of range

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Feb 1, 2021, 5:53:25 AM2/1/21

to leafcutter-users

Hello ,

I also followed the following advice, but still got the sam error message.

Hi,

firstly you need two dashes for adding arguments with more than one letter so it should be "--checkchrom".

secondly, if you still get errors with regtools -s 1 or -2, manually remove the "?" lines from your junctions.

If your junction files are all files ending in .junc you could do this:

for i in *junc; do

grep -v "?" $i > ${i}.trimmed.junc

done

Best wishes,

Aynur

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