Moderator: h.mon

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h.mon26k
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Posts by h.mon

<prev • 3,760 results • page 2 of 376 • next >
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Comment: C: operon for rRNA genes
... By "find their operons", you mean you want to find the genomic regions where they are located, and how many copies of the operon the draft genome has? If this is an Illumina-only draft assembly, I am afraid you won't be able to confidently ascertain both points above. ...
written 7 days ago by h.mon26k
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Comment: C: How to proceed after removing batch effect with limma?
... The [DESeq2 vignette][1] says the `limma::removeBatchEffect( )` function is used only for visualization. The **Quick start** section of the vignette already shows how to control for simple batch effects, the issue is discussed in other sections of the vignette as well. dds <- DESeqDataSetFr ...
written 7 days ago by h.mon26k
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Answer: A: Bowtie2 hg19 reference for gatk MuTect
... >Do I need to create new indices to be able to use this reference file from the GATK bundle with bowtie2? Yes, creating the bowtie2 indices would help. ...
written 8 days ago by h.mon26k
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Comment: C: Bowtie2 hg19 reference for gatk MuTect
... >The reference in GATK bundle (Homo_sapiens_assembly19.fasta) does not seem to work with Bowtie2 What make you think this reference doesn't work with Bowtie2? Do you encounter any errors? What were the steps you run? ...
written 8 days ago by h.mon26k
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Comment: C: InterProScan and HMMER - different results
... Do you know what is the exact HMMER command InterProScan is using? Do you know if / how InterProScan filters input and output? You may have to dig InterProScan logs to find out these details. ...
written 8 days ago by h.mon26k
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Comment: C: What to do if more than 78% of genes are differentially expressed according to D
... >because of extraction method, 78% of genes(all genes for that sp, up and down) are differentially expressed (extraction enriched some RNA number) Please explain this also. If what you say is true, and extraction method causes expression differences between treatments, then you can't untangle tr ...
written 8 days ago by h.mon26k
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Answer: A: Comparing contigs files and recover similar contigs
... You have two options: 1) You may try an assembly reconciliation or assembly merging. There are several tools for that, an internet search should help you find some. I haven't done an assembly reconciliation yet, but a recent review doesn't seem encouraging about its usefulness: [A comparative eval ...
written 9 days ago by h.mon26k
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Answer: A: Ion Torrent vs 454, Illumina and Pacbio reads
... 454 (now defunct) is the most similar technology to Ion Torrent, though there are important differences - an interesting source is [Beyond Generations: My Vocabulary for Sequencing Tech][1] - even though it doesn't discuss in detail how the different technologies are related. Some sources (e.g. [Al ...
written 12 days ago by h.mon26k
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Comment: C: Multi-mapping High with featureCounts but not STAR
... You can try StringTie, it will assemble novel transcripts based on the genome, and quantify known and novel transcripts. ...
written 14 days ago by h.mon26k
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Comment: C: Low pseudo-alignment rate with Kallisto
... First I would check for rRNA contamination, there are several threads here discussing methods to do so (e.g. https://www.biostars.org/p/288654/ ). RSeQC can also give some useful diagnostics, but you will have to map to the genome to use it. ...
written 16 days ago by h.mon26k

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