Comments (1)
Hi @sivico26 AlignQC can work on short read data. My inefficient use of memory is what prevents it from being easily applied to short read data. If you downsample your short reads to like 100k or maybe 1M reads it should work fine.
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Related Issues (20)
- ValueError HOT 14
- Adjust sort requirement to be compatible with any samtools sorted file HOT 1
- Isoforms
- Partial match/annotation HOT 6
- Error while reading reference fasta HOT 2
- Adapter sequences in reads
- Minimap2 compatibility HOT 3
- Error while reading index HOT 1
- ModuleNotFoundError: No module named 'analyze' HOT 4
- `bioconda` package HOT 3
- Error X11 module cannot be loaded
- input bam
- transcript read count from alignQC
- IOError: Not a gzipped file HOT 6
- Memory Requirements HOT 4
- ValueError: Expected lines to be ordered but they appear not to be ordered on line 49447 HOT 1
- Hi @rojinsafavi Sorry for the delay. I'm a busy these days so if lose track of these I appreciate getting the reminder :) It looks like a problem streaming the data. Is your alignment file sorted by genomic position? If they are ... I have a second more complicated problem that this may be due to. If they are supported by position, do you know if the index of your chromosomes are in alphabetical order? I notice that different aligners have different behaviors when it comes to sorting and sometimes they sort chromosomes alphabetically ... sometimes they do other things. And i may be making the alphabetical assumption in the ordering-check. Something you can try is my sort tool thats in seqtools
- Expected lines to be ordered but they appear not to be ordered HOT 1
- problem with the installation via Conda HOT 1
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