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Hi,
I am running DCC on an organism without an annotated mitochondrial chromosome. It does not matter if I run DCC with -M or not, it also breaks with -k and not, as well as -t and without. I tried v…
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Dear colleagues, I used NCLscan to detect circRNA molecules.
From what I understood this tool uses pseudo-references as a strategy to detect this kind of molecules.
All pseudo reference are construct…
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if checkjunctionfiles(options.Input, options.mate1, options.mate2):
logging.info("circRNA detection skipped due to empty junction files")
print("circRNA detection skipped due to empt…
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hi author:
The below words quoted from your website about characterization of Circular RNA Alternative Splicing
"It requires alignment results (set using -a) of poly(A)+ RNA-seq derived from the same…
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Hi,
I am getting this below error when running DCC. Could you help resolve this issue?
Traceback (most recent call last):
File "/home/ssekar/tools/circRNA/DCC-0.3.2/DCC/main.py", line 507, in
…
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unique mapping with TopHat-Fusion, tophat2 -o tophat_fusion -p 15 --fusion-search --keep-fasta-order --bowtie1 --no-coverage-search hg19_bowtie1_index tophat/unmapped.fastq, can i use bowtie2 to mapp…
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When I run DCC, I get an error with pybedtools groupby:
python2.7 /home/ehutchins/tools/DCC/DCC/main.py @chimeric_junctions -mt1 @chimeric_junctions_mate1 -mt2 @chimeric_junctions_mate2 -D -N -temp …
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md5sum:
bb39ad5a080b647ecf245ae126a8eb93 remote_drive/mir-count.csv
bb39ad5a080b647ecf245ae126a8eb93 local_drive/mir-count.csv
in python
import pandas as pd
print pd.**version**
-# Shows 0.17.1
L…
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Hi,
I found CIRCexplore a very useful tool for detecting circRNA from RNA-seq. I am interested in detecting circRNA which completely falls in intron (=lariat sequence). I mapped the paired-end reads …