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Hi,
Using slam-seq with mouse genome (option --genome GRCm38) I'm getting an error in the gtf2bed process :
Traceback (most recent call last):
File "/home/adminmanu/scratch/slamseq/bin/gtf2bed.py", line 50, in <module>
key, value = attribute.split(' ')
I found the guilty : One transcript (or may be more, I don't have check all transcripts) have with this attribute : "transcript_support_level 1 (assigned to previous version 2)"
I correct the script gtf2bed.py by adding the selection of the two first elements of attribute variable at the line 50 and 87 and this works :
key, value = attribute.split(' ')[:2]
I don't know if this solution can be export to all gtf...
Thanks !
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