User: Macspider

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Macspider1.1k
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Posts by Macspider

<prev • 240 results • page 1 of 24 • next >
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Best set of nucmer mapping parameters for genome vs genome alignment
... Hi all, I am currently using **nucmer** for a genome vs genome alignment. I'm tweaking with these parameters: - **-b|breaklen** = Set the distance an alignment extension will attempt to extend poor scoring regions before giving up (default 200) - **-l|minmatch** = Set the minimum length of a ...
nucleotide genome alignment parameters nucmer written 1 hour ago by Macspider1.1k
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Comment: C: Error when installing cufflinks
... You should probably do it with: export BAM_ROOT=/home/ubuntu/software/samtools-1.4.1/ However, if it says that it's not a valid directory, what does it say with: ls -l /home/ubuntu/software/samtools-1.4.1/ ls -l /home/ubuntu/software/samtools* ? ...
written 3 hours ago by Macspider1.1k
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Comment: C: what library preparation kit was used in sequencing process?
... When you run fastQC it will also tell you which illumina technology was used (like illumina 1.9 or illumina 1.5+). This is not a clear answer but can allow you to search which are the library preparation kits for such technologies, perhaps there is only one (i'm guessing). ...
written 3 hours ago by Macspider1.1k
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Comment: C: what library preparation kit was used in sequencing process?
... I don't think so, but have a look: https://support.illumina.com/help/SequencingAnalysisWorkflow/Content/Vault/Informatics/Sequencing_Analysis/CASAVA/swSEQ_mCA_FASTQFiles.htm ...
written 6 days ago by Macspider1.1k
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Comment: C: Output of featureCounts() is not integer
... Maybe a workaround: **htseq-count** outputs integer counts. ...
written 13 days ago by Macspider1.1k
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Comment: C: No positive results after SAM
... When this happens you should try with other tools as @b.nota suggested. Some suggestions: Limma: https://bioconductor.org/packages/release/bioc/html/limma.html DESeq2: https://bioconductor.org/packages/release/bioc/html/DESeq2.html EdgeR: https://bioconductor.org/packages/release/bioc/html/edgeR. ...
written 18 days ago by Macspider1.1k
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Comment: C: Using samtools to find mutation
... > its not helping Since it's probably the gold standard in the variant calling pipelines I highly doubt that it doesn't help... It does exactly what you need if you combine it with the other steps I mentioned. Can you post the command you ran? ...
written 18 days ago by Macspider1.1k
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Answer: A: bowtie2-align died with signal 6 (ABRT) (core dumped)
... Based on this discussion: https://lists.freebsd.org/pipermail/freebsd-questions/2004-April/042665.html > Signal 6 is SIGABRT -- see /usr/include/sys/signal.h. A process dying > with this signal is usually due to it calling the abort(3) function. > That generally indicates that the process ...
written 21 days ago by Macspider1.1k
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Comment: C: Difference in alignment summary from bam/sam and bed
... I have no ready explanation, but you could try to see if your awk pipe is working properly by reconverting the bed file to to bam with `bedtools bedtobam`: http://bedtools.readthedocs.io/en/latest/content/bedtools-suite.html After re-conversion, check again with flagstat. If you get the same numbe ...
written 21 days ago by Macspider1.1k
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Comment: C: Add something to change the transcripts ID
... Two remarks: 1. When you post some tabular file content like in this case, wrap it with the "code sample" option. It's the 5th button from the left of your message editor panel. 2. This is actually an easy task if you know a little bit of scripting. I would suggest you to learn some `python`, `pe ...
written 21 days ago by Macspider1.1k

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Student 13 days ago, asked a question with at least 3 up-votes. For DESeq2 proper design setting
Scholar 16 days ago, created an answer that has been accepted. For A: tophat --max-multihits impacts 'mapped in a proper pair'
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