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mlbendall / telescope

Quantification of transposable element expression using RNA-seq
MIT License
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make telescope faster #49

Open AlisaGU opened 1 year ago

AlisaGU commented 1 year ago

Hi, is there a way to make telescope faster? I have a big genome (47G) and my bam file from STAR is about 27G.

It seems that telescope will take a lot of time from the log file.

[E::idx_find_and_load] Could not retrieve index file for 'YPX55273S14A.STAR.K1000.Aligned.out.bam'
2023-10-11 09:46:51 INFO     ...processed 2.5M fragments                                  (from _print_progress in model.py:69)
2023-10-11 09:51:26 INFO     ...processed 5.0M fragments                                  (from _print_progress in model.py:69)
2023-10-11 09:56:05 INFO     ...processed 7.5M fragments                                  (from _print_progress in model.py:69)
2023-10-11 10:00:40 INFO     ...processed 10.0M fragments                                 (from _print_progress in model.py:69)
2023-10-11 10:05:17 INFO     ...processed 12.5M fragments                                 (from _print_progress in model.py:69)
2023-10-11 10:09:54 INFO     ...processed 15.0M fragments                                 (from _print_progress in model.py:69)
2023-10-11 10:14:31 INFO     ...processed 17.5M fragments                                 (from _print_progress in model.py:69)
AlisaGU commented 1 year ago

Can I split the bam into several files to speed up?

JianhuaWang95 commented 6 months ago

Hi Gu, When you run telescope with the bam file generated using STAR, will you get the error info: AssertionError: Missing ZT tag?