search

gx-health / TAGET

MIT License
5 stars 3 forks source link

The original file has not been changed #7

Open bingqiWu opened 5 months ago

bingqiWu commented 5 months ago

In TAGET-master/ISO_anno_V02.py, the original file has not been changed, i.e., gtf and bed file. gtf and bed file has not been changed

I wonder which gtf and bed file that I shoule use? Is it reference gtf? I used minimap2 to map the sample's fastq to the ref genome, and minimap2 generated the "sample.minimap2.bed". as the same time, TAGET also generate the "sample.annot.bed". So, I have no idea which bed file that I shoule use. Thank you for your reply in advance

bingqiWu commented 5 months ago

Although it outputed the error, it still finished the work. Is it ok? Won't it affect the result? `File "/data/workdir/wubq/software/TAGET-master//ISO_anno_combine.py", line 148, in db = ISO_anno_V02.load_pickle(gtf) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/data/workdir/wubq/software/TAGET-master/ISO_anno_V02.py", line 16, in load_pickle return pickle.load(open(file_in, 'rb')) ^^^^^^^^^^^^^^^^^^^ TypeError: expected str, bytes or os.PathLike object, not NoneType

Finished !`