Moderator: h.mon

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Posts by h.mon

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Comment: C: Trim Paired-end Fastq Files
... Where did you obtain the files? Did you download them from ENA / SRA? A sequencing facility sequenced your samples? You were given these files by a collaborator? Did you run FastQC on them? Seems like they may have been trimmed already. Some quick and dirty sanity checks - what is the output of: ...
written 51 minutes ago by h.mon16k
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Comment: C: mysql-8.0.11 parameter for mysql 5.1.7
... No, last time I did this analysis I used OrthoMCL, but I remember having problems with the MySQL install. OMA is a frequently used option, but I never used it. Unless there is a new page I am unaware of, OrthoMCL is inactive as well, the last release is version 2.0.9, from 2013-07-18. ...
written 7 hours ago by h.mon16k
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Comment: C: Finding orientation of single-ended reads (R or F)
... If you want to know which setting to use with trinity: 1) map some reads with STAR (you will need some 32-34Gb memory). The index has to be built with an annotation built-in, or you can provide an annotation at run time. You don't need to output a bam file, just the gene counts: STAR --outFi ...
written 7 hours ago by h.mon16k
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Answer: A: Obiconvert produces empty EcoPCR database...why?
... ECOPCROUTPUT / newsequences.fasta Remove the `/`: ECOPCROUTPUT newsequences.fasta ...
written 9 hours ago by h.mon16k
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Answer: A: Finding orientation of single-ended reads (R or F)
... Sometimes the information is found at each sample page, for example, for the first and last samples (I didn't look at the others): >Construction protocol: Agilent SureSelect Strand Specific RNA ...
written 9 hours ago by h.mon16k
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Comment: C: mysql-8.0.11 parameter for mysql 5.1.7
... OrthoMCL can be a pain to install, try [Proteinortho][1], or another tool. [PorthoMCL][2] implements the same algorithm as OrthoMCL, but drops the requirement for a database. [1]: https://www.bioinf.uni-leipzig.de/Software/proteinortho/ [2]: https://github.com/etabari/PorthoMCL/wiki ...
written 10 hours ago by h.mon16k
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Comment: A: How to install LigandScout software on Linux?
... You should contact their customer support, as it is a paid product. http://www.inteligand.com/contact/ ...
written 11 hours ago by h.mon16k
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Answer: A: To reassemble Illumina and PacBio, or just upgrade previous assembly with PacBio
... **edit:** As soon as I posted, it occurred to me it is probably better to perform a *de novo* hybrid assembly, as I think this has a better change of correcting small duplications which may have been misassembled on the Illumina-only assembly. **end of edit.** Probably depends on the coverage for ...
written 13 hours ago by h.mon16k
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Comment: C: how to evaluate coverage at a regions of interest and generate specificity, sens
... Do you have a bed file with exome probes? If you do, you can use bedtools to achieve several of your goals: > identify genes that may have low coverage because no probes are available Use [bedtools intersect -v][1] with the genome annotation to get the genes / exons not covered by the probes. ...
written 13 hours ago by h.mon16k
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Comment: C: Quick and easy way to get alignment stats from many SAM/BAM files?
... And `samtools flagstat`? ...
written 14 hours ago by h.mon16k

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Scholar 9 days ago, created an answer that has been accepted. For A: Script for extracting data from a tab-delimited file
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