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 8 months 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 9 months 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 9 months 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 9 months 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 9 months 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 10 months 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 10 months 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 10 months 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 10 months 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 10 months ago by michael.ante3.6k

Latest awards to michael.ante

Appreciated 6 months ago, created a post with more than 5 votes. For A: htseq-count output file
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: insert word in each row
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: insert word in each row
Commentator 11 months ago, created a comment with at least 3 up-votes. For C: Merge 2 files based on rs number but keep all info only from the first file
Commentator 12 months ago, created a comment with at least 3 up-votes. For C: Merge 2 files based on rs number but keep all info only from the first file
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: insert word in each row
Appreciated 18 months ago, created a post with more than 5 votes. For A: Can FPKM be added?
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Teacher 19 months ago, created an answer with at least 3 up-votes. For A: insert word in each row
Commentator 20 months ago, created a comment with at least 3 up-votes. For C: Merge 2 files based on rs number but keep all info only from the first file
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: insert word in each row
Commentator 21 months ago, created a comment with at least 3 up-votes. For C: Merge 2 files based on rs number but keep all info only from the first file
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Scholar 23 months ago, created an answer that has been accepted. For A: questions on rna-seq data analysis
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