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(TEPID) ruoruo@DESKTOP-5SC16P5:/mnt/d/tepid-discover$ tepid-discover -p 16 -c XXX.bam -s XXX.split.bam -n XXX -t TE.bed Processing XXX Running paired-end mode Estimating mean insert size and coverage Warning: coverage may not be sufficiently high to reliably discover polymorphic TE insertions mean insert size = 356 bp, standard deviation = 67 bp coverage = 1x read length = 143 bp Processing split reads Finding discordant reads Processing TE annotation Finding deletions ***** WARNING: File /tmp/pybedtools.Ny7kTr.tmp has inconsistent naming convention for record: contig_100 278 341
***** WARNING: File /tmp/pybedtools.Ny7kTr.tmp has inconsistent naming convention for record: contig_100 278 341
Finding insertions Error: no reads intersecting TEs found
How could I solve it
The text was updated successfully, but these errors were encountered:
coverage = 1x it is so low.
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(TEPID) ruoruo@DESKTOP-5SC16P5:/mnt/d/tepid-discover$ tepid-discover -p 16 -c XXX.bam -s XXX.split.bam -n XXX -t TE.bed
Processing XXX
Running paired-end mode
Estimating mean insert size and coverage
Warning: coverage may not be sufficiently high to reliably discover polymorphic TE insertions
mean insert size = 356 bp, standard deviation = 67 bp
coverage = 1x
read length = 143 bp
Processing split reads
Finding discordant reads
Processing TE annotation
Finding deletions
***** WARNING: File /tmp/pybedtools.Ny7kTr.tmp has inconsistent naming convention for record:
contig_100 278 341
***** WARNING: File /tmp/pybedtools.Ny7kTr.tmp has inconsistent naming convention for record:
contig_100 278 341
Finding insertions
Error: no reads intersecting TEs found
How could I solve it
The text was updated successfully, but these errors were encountered: