User: pengchy

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pengchy430
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China/Beijing
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3 days, 7 hours ago
Joined:
8 years, 3 months ago
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Posts by pengchy

<prev • 108 results • page 1 of 11 • next >
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Comment: C: bowtie error in align_and_estimate_abundance.pl job
... As the error message said "Warning: Empty input file", the input file for bowtie-build is empty. Please check the corresponding input file, you will find the size of the input file is 0. So the input file is wrongly produced. ...
written 3 months ago by pengchy430
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Comment: C: Trim bam file reads to the same length
... Hi @genomax, it turned out to be the java version's problem. jdk1.8 work, but 1.7 failed. I modified the line 228 in the file *bbmap/reformat.sh* as following: ` local CMD="/path/to/java/jdk1.8.0_211/bin/java $EA $EOOM $z $z2 -cp $CP jgi.ReformatReads $@"` ...
written 4 months ago by pengchy430
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Comment: C: Trim bam file reads to the same length
... Hi @genomax, please help check the following error. I have installed the bbmap and don't remove any files from the installion directory reformat.sh in=test.bam out=test_short.bam maxlength=75 /histor/kang/yangpc/soft/01.NGS_data_process/bbmap//calcmem.sh: line 75: [: -v: unary operator expe ...
written 5 months ago by pengchy430
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Answer: C: How convert files .psl to files .bed?
... https://www.biostars.org/p/215194/#421038 In that thread, I recommend replacing blat by gmap to perform mapping, gmap could output the alignment result in multiple format, including psl, gff3 and bed. So the conversion between psl and gff would no longer be needed. ...
written 7 months ago by pengchy430
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Comment: A: Convert BLAT to GFF file?
... Another alternative method is using Gmap alignment tools with GFF output format -f, --format=INT Other format for output (also note the -A and -S options and other options listed under Output types): psl ...
written 7 months ago by pengchy430
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Answer: A: Package to classify LncRNA into LncRNAs, intronic LncRNAs and antisense LncRNAs
... Please have a look at [`gffcompare`][1], through which genomic gff file could be used as reference ("-r"). [1]: https://ccb.jhu.edu/software/stringtie/gffcompare.shtml ...
written 14 months ago by pengchy430
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Comment: C: How To Interpret The Results Produced By Verify3D Structure Evaluation Server?
... The new web service of Verify 3D is available [here][1] [1]: http://servicesn.mbi.ucla.edu/Verify3D/ ...
written 18 months ago by pengchy430
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stand-alone pre-miRNA prediction packages
... Hi, after a while searching and investigation, I couldn't found a user-friendly available package for pre-miRNA prediction or classification, although large number of this kind of packages have been published since 2003. The following packages have been tested failed. - Triplet-SVM: Need contact t ...
prediction pre-mirna stand-alone package written 20 months ago by pengchy430
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Comment: C: Problem ViennaRNA package install
... Please provide the full log information of "configure" and "make". ...
written 20 months ago by pengchy430
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Answer: C: Alternative tools for PacBio collapse_isoforms_by_sam.py
... This problem has been resolved by installation of: [cDNA_Cupcake][1], which is easy to install and also contains collapse_isoforms_by_sam.py script [1]: https://github.com/Magdoll/cDNA_Cupcake/wiki ...
written 2.1 years ago by pengchy430

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Scholar 2.1 years ago, created an answer that has been accepted. For A: import stke pathway xml file into cytoscape
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