User: venura

gravatar for venura
venura60
Reputation:
60
Status:
Trusted
Location:
University of Peradeniya
Twitter:
venuraherath
Scholar ID:
Google Scholar Page
Last seen:
15 hours ago
Joined:
1 year, 1 month ago
Email:
v*****@agri.pdn.ac.lk

Posts by venura

<prev • 59 results • page 1 of 6 • next >
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Answer: A: Bulk extraction of cis-elements (TFBS) from Softberry output
... Figured out. I added the code below so f someone wants to do the same. with open('Softberry.txt') as f: for line in f: if line.startswith(' QUERY:'): query = line.split(':', 1)[1].strip() if 'AC:' in line: ac = line.split('AC:')[1].split(':')[0].strip ...
written 24 days ago by venura60
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Bulk extraction of cis-elements (TFBS) from Softberry output
... Hi, I have a document (its 100 pages long and only two instances were displayed below) with the following output came from NSite (softberry); QUERY: STBZIP38 Length of Query Sequence: 2000 bp | Nucleotide Frequencies: A - 0.34 G - 0.16 T - 0.35 C - 0.15 ...
python bash written 25 days ago by venura60
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Answer: A: Stringtie 2.1.4: Error running prepDE.py
... I ran `prepDE.py -i ballgown` and got the output. ...
written 29 days ago by venura60
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Stringtie 2.1.4: Error running prepDE.py
... Hi , When I run prepDE.py job exit with the following error. I am using StringTie/2.1.4 with Python/2.7.18. Traceback (most recent call last): File "/sw/eb/software/StringTie/2.1.4-GCC-9.3.0/bin/prepDE.py", line 58, in samples = [(i,glob.iglob(os.path.join(opts.input,i,"*.gtf")).next()) for i in n ...
stringtie written 4 weeks ago by venura60
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Answer: A: Stringtie Error: Getting the input alignment file is not sorted! even though fil
... After communicating with the author, found out that the above error is a bug found in version 2.1.3. Problem solved after updating to ver 2.1.4. ...
written 4 weeks ago by venura60
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Comment: C: Stringtie Error: Getting the input alignment file is not sorted! even though fil
... I ran `samtools index PVX_2d_1.bam` followed by `samtools view -H PVX_2d_1.bam | grep "HD"` and got the following (same as earlier) > @HD VN:1.0 SO:coordinate Hope I didn't misunderstand what you asked me to do. ...
written 4 weeks ago by venura60
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Stringtie Error: Getting the input alignment file is not sorted! even though file is sorted
... Hi, I am getting the following error when I try to use the Stringtie merge function: stringtie --merge -p $threads -G DM_1-3_516_R44_potato.v6.1.working_models.gff3 -o stringtie_merged.gtf mergelist.txt > Error: the input alignment file is not sorted! Alignments (7) already found for sc ...
stringtine samtools written 4 weeks ago by venura60
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Comment: C: HISAT2: Question regarding providing file path to indexed genome folder
... Everything is running fine and got bam files too. :) The only exception is the following (I guess it is something to with installation at ADA cluster since I don't see such script there) > /sw/eb/software/HISAT2/2.2.0-foss-2018b/bin/hisat2_read_statistics.py: No such file or directory (ERR) PS: ...
written 4 weeks ago by venura60
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Comment: C: HISAT2: Question regarding providing file path to indexed genome folder
... Oh, Shoot! You are correct. Still learning A, B, Cs.. ...
written 4 weeks ago by venura60
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Comment: C: HISAT2: Question regarding providing file path to indexed genome folder
... Will do the needful and Get back with the outcome! Thanks a lot, ATpoint! 🙏 ...
written 4 weeks ago by venura60

Latest awards to venura

Scholar 24 days ago, created an answer that has been accepted. For A: MCScanx is giving an Empty Output (even for example files)
Scholar 24 days ago, created an answer that has been accepted. For A: MCScanx is giving an Empty Output (even for example files)
Scholar 24 days ago, created an answer that has been accepted. For A: Bulk extraction of cis-elements (TFBS) from Softberry output
Supporter 5 weeks ago, voted at least 25 times.
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: MCScanx is giving an Empty Output (even for example files)
Scholar 13 months ago, created an answer that has been accepted. For A: MCScanx is giving an Empty Output (even for example files)

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