User: mbens

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mbens100
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100
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Germany
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7 months, 3 weeks ago
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9 months, 2 weeks ago
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Posts by mbens

<prev • 9 results • page 1 of 1 • next >
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Comment: C: Fastq files quality
... Were all samples (files) sequenced on the same lane or in the same sequencing run? Generally, for read data obtained from Illumina sequencers, you would expect good quality in the midsection and lower quality at the ends of reads. So a quality drop in the midsection might indicate some failure (air ...
written 8 months ago by mbens100
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Answer: A: How to merge probes with the same gene symbol in soft file?
... There is no general rule on how to deal with such probe sets in microarray data. Different probes mapping to the same gene symbol might correspond to different isoforms of that genes and are meaningful to analyse separately. Other probes might be prone to cross-hybridization and should probably be r ...
written 9 months ago by mbens100
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Comment: C: In gff3 format, could one eukaryotic mRNA contain more than one protein coding s
... I don't understand how that is different. Do you mean polycistronic transcripts? Or maybe uORFs (Upstream Open Reading Frame)? In case of polycistronic transcripts: - define both genes (and assign different ID attributes, e.g. ID=geneA and ID=geneB) - define a single mRNA feature (e.g. ID=mrna ...
written 9 months ago by mbens100
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Answer: A: How to represent two CDSs for one eukaryotic mRNA in the gff3 format?
... In principle, you can define an arbitrary number of CDS per mRNA. The Parent attribute of each CDS indicates to which mRNA it belongs. If your CDS feature spans multiple lines (discontinuous features) it must have an ID to indicate lines that collectively represent the CDS. In fact, your example alr ...
written 9 months ago by mbens100
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Answer: A: de novo exon-exon junction identification tool from transcriptome assembly
... You could align your contigs to the genome sequence of a closely related species to identify exon boundaries. There are a variety of spliced aligners available and were compared for instance in > Iwata H, Gotoh O. Benchmarking spliced alignment programs including > Spaln2, an extended version ...
written 9 months ago by mbens100
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Answer: A: Why do PFAM alignments contain 'X'?
... The nomenclature for amino acids includes 'X' for 'unknown amino acid' ([IUPAC](https://www.iupac.org/publications/pac/1984/pdf/5605x0595.pdf)). According to Uniprot, second amino acid of [G1N5G7_MELGA](http://www.uniprot.org/uniprot/G1N5G7) is unknown. ...
written 9 months ago by mbens100
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Comment: C: Counting reads in CDS - but skipping few first/last codons
... More specifically: [`bedtools slop`](https://bedtools.readthedocs.io/en/latest/content/tools/slop.html) is able to increase the size of features. However, using negative integers for `-l` and `-r` shrinks features at the desired end. ...
written 9 months ago by mbens100
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Answer: A: Input preparation for PAML analysis
... [Gblocks](http://molevol.cmima.csic.es/castresana/Gblocks_server.html) is able to remove poorly aligned regions and gaps from alignments. > Castresana, J. (2000). Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Molecular Biology and Evolution 17, ...
written 9 months ago by mbens100
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Answer: A: How can I run lastz on multiple files using a bash loop and an associative array
... It depends on the location of your reference files. Assuming reference and sample are located within one directory, you won't need associative arrays. Example file structure: ├── a │ ├── reference.fasta │ └── sample.fasta ├── b │ ├── reference.fasta │ └── sample.fas ...
written 9 months ago by mbens100

Latest awards to mbens

Scholar 9 months ago, created an answer that has been accepted. For A: How can I run lastz on multiple files using a bash loop and an associative array
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: How can I run lastz on multiple files using a bash loop and an associative array
Scholar 9 months ago, created an answer that has been accepted. For A: How can I run lastz on multiple files using a bash loop and an associative array
Scholar 9 months ago, created an answer that has been accepted. For A: How can I run lastz on multiple files using a bash loop and an associative array
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: How can I run lastz on multiple files using a bash loop and an associative array

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