Comments (1)
Dear Stephen,
Different library has different deep. If you want to shorten your sRNA length, you should change the parameters for transcript detection, not sRNA detection. sRNA detection is based on the list of transcripts. Thus, if the transcript does not overlap the known genes and the length of transcript is within proper sRNA range, it will be assigned as sRNA candidates. Li_ANNOgesic_154 looks like a long transcript, but includes a lot of relative low coverage values. Probably, you have deep libraries, so the coverage values of the low expression region may be still higher than 10. You can raise up the cutoff of coverage for transcript detection ("--height" for subcommand "transcript", default is 10). You can also change "--tolerance" if you feel the transcripts become too fragmental. You can play around the parameter to define your ideal setting. In order to reduce the running time, you can just use one or two libraries for testing.
Best,
Sung-Huan
from annogesic.
Related Issues (20)
- too many warnings in target prediction HOT 6
- sRNA prediction error HOT 14
- Transcript detection error HOT 7
- Merging results srna_target, wrong column names HOT 2
- optimization of TSS error HOT 8
- Path to instal sgemehl in get_package_database.sh is old HOT 1
- optimize_tss_ps error:TypeError: int() argument must be a string, a bytes-like object or a number, not 'NoneType' HOT 6
- Installation directory
- --tex_notex_libs was assinged incorrectly HOT 6
- Read-only file system HOT 1
- TSSpredator error HOT 6
- TAP-only (no TEX) dRNA-seq datasets HOT 2
- tex_notex_libs formatting HOT 4
- TSSpredator-1.06.jar not found during Docker build HOT 1
- annogesic: error: unrecognized arguments: --tsspredator_jar TSSpredator-1.1beta.jar HOT 3
- Use normalized or raw coverage files for ANNOgesic? HOT 1
- annogesic tss_ps: understanding the "--condition_names" error HOT 1
- annogesic from nanopore transcriptomic output HOT 2
- sRNA target prediction error HOT 5
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