User: michael.ante

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michael.ante3.6k
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Posts by michael.ante

<prev • 408 results • page 1 of 41 • next >
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Comment: C: How to identify 3'UTR region?
... Hi, it's more a vague idea: You can try to find the PAS-signal and define the region between it and the CDS as 3' UTR. The signal is usually an A-rich hexamer. You may model the genome with a similar species' 3' UTR-length distribution to limit the search space. Cheers, Michael ...
written 11 days ago by michael.ante3.6k
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Comment: C: featureCounts log: "WARNING contig is not found in the provided genome file!"
... Is the chromosome/config name identical in both files? Does it contain spaces like `HanXRQCP 123456bp further information`? Are the names from the alignment altered? ...
written 20 days ago by michael.ante3.6k
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Answer: A: How to interpret the differences of read counts using htseq and feature counts?
... Hi , You are using the default values for quality filtering. Leading to different levels of stringency: > __too_low_aQual 2391179 vs > Unassigned_MappingQuality 0 The default mapping quality's minimum is 10 for htseq-count and 0 for featureCounts. Using the same quality filter value ...
written 5 weeks ago by michael.ante3.6k
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Comment: C: Would curated pathway gene set better being weighted than being binary
... To my understanding, having the fitting gene expression profile is the necessary condition, that a pathway might be activated in your sample. But it's not the sufficient condition. Some enzymes might be present, but in an inactive state. To make some robust statements, you can correlate the gene ex ...
written 5 weeks ago by michael.ante3.6k
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Comment: C: Would curated pathway gene set better being weighted than being binary
... Hi CY, I'd guess that would be true if there is a direct relationship between gene expression and enzyme-activity (which is more or less the same for all genes). You have also the ambiguity between gene-centered pathway annotation and expression of gene isoforms which might or might not different ...
written 5 weeks ago by michael.ante3.6k
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Comment: C: Extract sequences from fastA files based on csv chart in R
... Apparently, there is an R-package for reading and accessing fasta files [seqinr][1]. Once having the fasta as object, you it should be easy to apply your Perl routines. [1]: https://www.rdocumentation.org/packages/seqinr/versions/3.6-1 ...
written 9 weeks ago by michael.ante3.6k
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Comment: C: Extract sequences from fastA files based on csv chart
... I guess that should be solvable by writing a script in biopython utilising the seqIO library. Alternatively, you can try it with command line tools like awk, cut, [fasgrep][1], and join to loop over you CSV file. [1]: https://github.com/tlawrence3/FAST/blob/master/README.md ...
written 9 weeks ago by michael.ante3.6k
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Comment: C: Error in piRNA gtf file while featurecounts step in STAR aligner?
... Hi Geetha, Did you receive an error? Can you provide the first couple of lines from your input and output gtf? ...
written 9 weeks ago by michael.ante3.6k
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Comment: C: STAR error (segmentation fault) in Aligning reads
... Usually, STAR needs a lot of RAM to align and even more to build the index. Thus, having the STAR index files properly generated, you should be able to run the alignment. Are there any clues in the log files from STAR, what went wrong? Have you tried it with R1 reads only? ...
written 9 weeks ago by michael.ante3.6k
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Comment: C: FASTQ exctract ID's
... Not the nicest solution, bit you can use grep to get the fastq entries: grep -f name.lst -A 3 --no-group-separator in.fq > out.fq The `-f` determines the name.lst entries as things to be searched for, `-A 3` leads to reporting the 3 lines **a**fter each hit. The `--no-group-separator`is not ...
written 9 weeks ago by michael.ante3.6k

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