Moderator: h.mon

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Posts by h.mon

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Comment: A: Error : samtools tiview
... `samtools tview` is not the most powerful genome browser available, I would recommend IGV, IGB or Tablet (among others) to get a richer view of alignments. How is the result wrong? You mean the long stretch of Ns? Try going to some position - press `g` then write down the position, something like ...
written 1 day ago by h.mon9.0k
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Comment: C: randomly shuffle BAM file
... Just to point out `samtools bamshuf` is found only up to SAMtools 1.2, from SAMtools 1.3 on, the command is `samtools collate`. In addition, `samtools collate` does output to stdout (I didn't test with bamshuf but maybe works too), but it needs to create the intermediary files nonetheless. samt ...
written 1 day ago by h.mon9.0k
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Comment: C: Error in running QoRTs after hisat2 alignment
... If you don't have more memory, I am afraid you run out of options. ...
written 1 day ago by h.mon9.0k
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Answer: A: RSeQC installation error
... Try with `virtualenv` and `pip`: virtualenv $HOME/.local/RSeQC-2.6.4 source $HOME/.local/RSeQC-2.6.4/bin/activate # I had to install nose first, otherwise dependency resolution would fail pip install nose pip install RSeQC==2.6.4 To use it: source $HOME/.local/RSeQC-2.6.4/ ...
written 1 day ago by h.mon9.0k
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Answer: A: Forward and Reverse Reads Out of Order
... Try [repair.sh][1] from the BBTools / BBMap suite: repair.sh in1=broken1.fq in2=broken2 out1=fixed1.fq out2=fixed2.fq outs=singletons.fq repair Read the guide and pay attention to memory usage. Depending on how much your files have been messed up, it may be worth starting over, this time proce ...
written 2 days ago by h.mon9.0k
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Answer: A: Tools to create workflows
... LMGTFY: [http://lmgtfy.com/?q=bioinformatics+workflows][1] Also, see this thread: [Which Bioinformatic Friendly Pipeline Building Framework?][2] [1]: http://lmgtfy.com/?q=bioinformatics+workflows [2]: https://www.biostars.org/p/91301/ ...
written 2 days ago by h.mon9.0k
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Answer: A: Deseq2 library load error
... Install GenomeInfoDbData: source("https://bioconductor.org/biocLite.R") biocLite("GenomeInfoDbData") In addition, you may want to recompile your BioConductor packages, see section `Recompiling installed Bioconductor packages` at [https://www.bioconductor.org/install/][1]. [1]: https:// ...
written 2 days ago by h.mon9.0k
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Comment: C: Blast2Go - Running Jobs in the Background
... Run Blast and InterProScan outside of Blast2GO and import the results. ...
written 2 days ago by h.mon9.0k
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Answer: A: bowtie2 : different MAPQ if -k is set
... Although I don't recall exactly how mapping quality is calculated for Bowtie2 default mode (search BioStars, there were some threads about this in the recent past), the manual clearly states that the `-k` parameters alters quality mapping calculation: > -k > > > > By default, bo ...
written 2 days ago by h.mon9.0k
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Answer: A: Error "Can't locate List/MoreUtils.pm in @INC"
... Use cpan or cpanm to install the List::MoreUtils module: cpanm List::MoreUtils Depending on your system, you may need to be root. If that is the case, you may install Perl on the same conda environment as you installed Blast, then install the module with cpan or cpanm. ...
written 2 days ago by h.mon9.0k

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Teacher 2 days ago, created an answer with at least 3 up-votes. For A: BWA -> samtools pipe while filtering mapped & unmapped reads
Scholar 2 days ago, created an answer that has been accepted. For A: BWA -> samtools pipe while filtering mapped & unmapped reads
Scholar 9 days ago, created an answer that has been accepted. For A: BWA -> samtools pipe while filtering mapped & unmapped reads
Commentator 12 days ago, created a comment with at least 3 up-votes. For C: RCurl instalation problem
Commentator 12 days ago, created a comment with at least 3 up-votes. For C: RCurl instalation problem
Teacher 19 days ago, created an answer with at least 3 up-votes. For A: Hi blog how to calculate differntial expression analysis if thre is no replicate
Commentator 19 days ago, created a comment with at least 3 up-votes. For C: RCurl instalation problem
Scholar 21 days ago, created an answer that has been accepted. For A: blastn doesn't consider the entire sequence
Teacher 21 days ago, created an answer with at least 3 up-votes. For A: Hi blog how to calculate differntial expression analysis if thre is no replicate
Scholar 21 days ago, created an answer that has been accepted. For A: Script for extracting data from a tab-delimited file
Scholar 21 days ago, created an answer that has been accepted. For A: Extract fasta sequences from a large file using a list of names
Scholar 21 days ago, created an answer that has been accepted. For A: Hey any one used QC-Chain tool?
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: Hi blog how to calculate differntial expression analysis if thre is no replicate
Scholar 6 weeks ago, created an answer that has been accepted. For A: Script for extracting data from a tab-delimited file
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Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: Hi blog how to calculate differntial expression analysis if thre is no replicate
Scholar 6 weeks ago, created an answer that has been accepted. For A: Script for extracting data from a tab-delimited file
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: Hi blog how to calculate differntial expression analysis if thre is no replicate
Scholar 7 weeks ago, created an answer that has been accepted. For A: Script for extracting data from a tab-delimited file
Scholar 7 weeks ago, created an answer that has been accepted. For A: Script for extracting data from a tab-delimited file
Scholar 7 weeks ago, created an answer that has been accepted. For A: Script for extracting data from a tab-delimited file
Scholar 7 weeks ago, created an answer that has been accepted. For A: Script for extracting data from a tab-delimited file
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: Hi blog how to calculate differntial expression analysis if thre is no replicate
Scholar 7 weeks ago, created an answer that has been accepted. For A: Script for extracting data from a tab-delimited file

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