Activity for mirPRo
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Jieming Shi posted a comment on discussion General Discussion
(1) HTSeq is only tested on version 0.6.1p1. Please try this version. (2) Please try to use FASTQ file as input when you do the mapping to generate SAM file.
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Sureshkumar Venkadesan posted a comment on discussion General Discussion
am using mirpro pipeline. It's giving quality string missing error in the htseq-count command. Error: Error occured when processing SAM input (line 17 of file Result/run/File.sam): Quality string missing [Exception type: ValueError, raised in _HTSeq.pyx:883]
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Please test with RNAfold version 2.1.9+.
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The gcc version should be 4.9+.
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Oleg posted a comment on discussion General Discussion
Hi! I am trying to run mirPro on the example data set, however I get following error:...
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User manual
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mirPRo released /mirPRo.1.1.4.tgz
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Raw Read Quality Filtering using FASTX-Toolkit of miRNA-Seq data
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update readme
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Tina O'Grady posted a comment on discussion General Discussion
Hello, I'm trying to run mirPRo on a cluster. I've installed all the prerequisite...
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update user manual
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update user manual
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remove platform dependent function; fix bug
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User manual
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fix bug and update readme
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1) yes 2) I suggest you skip this step. Sent from my iPhone On Aug 12, 2016, at 6:28...
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Hardik Modi posted a comment on ticket #7
Thanks. Two questions 1) All the subsequent analysis of human miRNA data is after...
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When the paper was published, miRPro had some bugs. One bug is that we used "fastq_quality_filter...
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Raw Read Quality Filtering using FASTX-Toolkit of miRNA-Seq data
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Q.7: How to use read alignment BAM files to obtain mirPRo known miRNA quantification results?
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Shi Jiu committed [6401dd]
version 1.1.2; improved error msg and mirpro_qu...
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User manual
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Q.7: How to use read alignment BAM files to obtain mirPRo known miRNA quantification results?
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Q.6: How to use read alignment BAM files to obtain mirPRo known miRNA quantification results?
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Error in mirPRo while novel study
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User manual
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version 1.1.1; fixed bugs
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initial commit for version 1.1
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User manual
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mirpro_gff3_to_gtf bug
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Fixed bug.
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Hello, mirPRo supports some of the parameter settings of novoaligh (version V3.02.12)....
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Pravin Nilawe posted a comment on ticket #6
Hello, Thanks for your help and suggestions. I was able to run the software successfully....
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Hi, As i was going through analysis, I was thinking if we can utilize the files created...
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Thanks everyone. I have just used this option and started an analysis. I would get...
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You are right. "--other" is necessary for novel miRNA prediction.
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tiennes modified a comment on ticket #6
I had the same problem, this resulted from forgetting to pass the option --other...
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I had the same problem, this resulted from forgetting to pass the option --other...
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Can you tell me the command you used to run this program?
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The version is V3.02.12. still its giving the error. On Thu, Apr 21, 2016 at 8:40...
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Version is V3.02.12. Still the problem exists.
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Please check the novoalign version. It should be release V3.02.12.
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Error in mirPRo while novel study
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Hello, We have certain data sequenced from Ion Proton system. I was trying to perform...
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User manual
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User manual
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mirPRo does not work with Sanger-encoded quality scores in fastq
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Please install the correct version of prerequisite tool described in wiki page.
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Kieran posted a comment on ticket #5
Hmm ... seems like this was because we were running an old version of the fastx toolkit....
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mirPRo does not work with Sanger-encoded quality scores in fastq
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User manual
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User manual
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User manual
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liangc_mu created ticket #4
mirpro_gff3_to_gtf bug
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Q.5: Where to find the read alignment file (mapped to known miRNA precursors) ?
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Q.6: How to test mirPRo?
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Q.6: How to test mirPRo?
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Q.6. How to test mirPRo?
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Q.6. How to test mirPRo?
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Q.5. Where to find the read alignment file (mapped to known miRNA precursors) ?
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Q.5. Where to find the read alignment file (mapped to known miRNA precursors) ?
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Q.5. Where to find the read alignment file (mapped to known miRNA precursors) ?
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Q.4: How can we conduct differential gene expression analysis using mirPRo result?
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Q.5. Where to find the read alignment file (mapped to known miRNA precursors) ?
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Q.4: How can we conduct differential gene expression analysis using mirPRo result?
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Q.3: How does the program calculate the miRNA gene expression level?
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Q.2: What's the biological meaning of the mature miRNA counts in each library?
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Q.1: Why not count reads mapped to the reverse strand of the precursor miRNA?
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Compatible issue with different sources and formats of genome annotation
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In the version of 20150930, mipro_feature_pro is capable to accept input files in...
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We found that some aligners (e.g., GSNAP) will tag a read with "NH:i:1" even this...
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mirpro_feature_pro bug
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mirpro_gff2gtf
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In version 20150930, we have created a new program mirpro_gff3_to_gtf, which can...
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mirpro_gff2gtf
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User manual
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User manual
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User manual
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User manual
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User manual
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User manual
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User manual
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User manual
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User manual
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User manual
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User manual
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User manual
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Q.3: How does the program calculate the miRNA gene expression level?
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Q.2: What's the biological meaning of the mature miRNA counts in each library?
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Q.1: Why not count reads mapped to the reverse strand of the precursor miRNA?
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Q&A.1 Why not count reads mapped to the reverse strand of the precursor miRNA?
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User manual
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User manual
