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3DGenomes / TADbit

TADbit is a complete Python library to deal with all steps to analyze, model and explore 3C-based data. With TADbit the user can map FASTQ files to obtain raw interaction binned matrices (Hi-C like matrices), normalize and correct interaction matrices, identify and compare the so-called Topologically Associating Domains (TADs), build 3D models from the interaction matrices, and finally, extract structural properties from the models. TADbit is complemented by TADkit for visualizing 3D models
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Mapping problem tutorial #373

Closed manuelfmerino closed 2 years ago

manuelfmerino commented 2 years ago

Hello,

I am running the tutorial, but I got stuck running the mapping. When I try to do so, the following errors arise:

File "G_1_map_iterative_rep_1.py", line 18, in tempdir='results/iterativ/{0}{1}/01mapping/mapped{0}_{1}_r1_tmp/'.format(cell, rep))

File "/users/manfernandez/.conda/envs/py37/lib/python3.7/site-packages/pytadbit/mapping/full_mapper.py", line 628, in full_mapping light_storage=light_storage)

File "/users/manfernandez/.conda/envs/py37/lib/python3.7/site-packages/pytadbit/mapping/full_mapper.py", line 225, in transform_fastq header, seq, qal = get_seq(header)

File "/users/manfernandez/.conda/envs/py37/lib/python3.7/site-packages/pytadbit/mapping/full_mapper.py", line 49, in _get_fastq_read_heavy seq = next(fhandler)

StopIteration

I ran the indexing using GEM 2 and installed TADbit 1.0.1 using Conda on Python 3.7.

Thanks a lot, Manuel F. Merino

EDIT: I found out that there's a mismatch between the number of lines in my files originally downloaded using fastq-dump (400000000 lines, i.e. 100M reads) and the files after the dsrc compression (400840880 lines), when checked using the command dsrc d -s FASTQs/mouse_B_rep1_1.fastq.dsrc | wc -l. Moreover, when I checked the last lines of my compressed file, I noted that it doesn't end with the read #100000000. Instead, the last line corresponds to the read #97829587. I am now considering that the dsrc compression is messing with my files. Could that be a possibility? I installed and used the program as explained in the TADbit installation guide and tutorial.

david-castillo commented 2 years ago

Hi Manuel,

We've never had that kind of problems with dsrc. Try to use a gzip file for the fastqs or directly the fastq file uncompressed and check if the tutorial works.

Regards

David

manuelfmerino commented 2 years ago

Hi David,

I tried using gzip compression and everything works fine. I actually suspect that fastq-dump could have been messing with the files in the download process, but I didn't fully dive into the problem. I guess I'm okay for now not having to use it.

Cheers and thanks a lot, Manuel