Intron clustering error

[Bio Comp]

Dear leafcutter users

Hello this is KyoungJun Lee who is new to leafcutter.

There is an index error during intron clustering but I could not catch the reason.

the command was:

python leafcutter_cluster_regtools.py --checkchrom -j juncs23.txt -m 50 -o ko23 -l 500000

and the result was shown as below:

scanning E100004016_L01_1_.junc...

scanning E100004016_L01_2_.junc...

scanning E100004016_L01_3_.junc...

scanningE100004016_L01_4_.junc...

scanning E100004016_L01_25.junc...

scanningE100004016_L01_33.junc...

Parsing...

chrX:-..chr22:-..chr11:-..chr15:-..chr18:+..chr3:-..chr16:+..chr5:-..chr20:+..chr19:-..chr13:+..chr8:-..chrY:+..Traceback (most recent call last):

  File "leafcutter_cluster_regtools.py", line 534, in <module>

    main(options, libl)

  File "leafcutter_cluster_regtools.py", line 14, in main

    pool_junc_reads(libl, options)

  File "leafcutter_cluster_regtools.py", line 72, in pool_junc_reads

    clu = cluster_intervals(read_ks)[0]

  File "leafcutter_cluster_regtools.py", line 337, in cluster_intervals

    current = E[0]

IndexError: list index out of range

Despite the --checkchrom option, it still give the same error. could you give any suggestion?

Thank you in advance.

KyoungJun

[countja...@gmail.com]

Hi KyoungJun,

this is a known issue and I've made a pull request to fix it: https://github.com/davidaknowles/leafcutter/pull/162 

The issue is caused by regtools assigning a "?" in the stand field to a small minority of your junctions.

Currently, there are two solutions:

1) rerun regtools junctions extract using the correct stranding parameter for your libraries (-s 1 or -s 2, see regtools documentation)

2) manually remove lines in your junction file with "?" by using something like 'grep -v "?" file.junc > new_file.junc'

best wishes,

Jack

[Елена Шарова]

-s 1 or 2 for stranded libraries doesn't help - I tried. I still receive  errors

[Елена Шарова]

I tried to ignore non-canonical chromosomes by adding -checkchrom  

IOError: No such file o directory 'heckchrom'

[countja...@gmail.com]

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,

Jack

[Елена Шарова]

I don't have lines with "?"  - I checked it

Two dashes works - thanks a lot!

[countja...@gmail.com]

wonderful to hear!