User: michael.ante
michael.ante • 3.6k
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Posts by michael.ante
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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.ante • 3.6k
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... 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.ante • 3.6k
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... 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.ante • 3.6k
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... 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.ante • 3.6k
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... 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.ante • 3.6k
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... 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.ante • 3.6k
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... 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.ante • 3.6k
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... 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.ante • 3.6k
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... 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.ante • 3.6k
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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.ante • 3.6k
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11 months ago,
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For C: Merge 2 files based on rs number but keep all info only from the first file
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For C: Merge 2 files based on rs number but keep all info only from the first file
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For C: Merge 2 files based on rs number but keep all info only from the first file
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For C: Merge 2 files based on rs number but keep all info only from the first file
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For C: Merge 2 files based on rs number but keep all info only from the first file
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For A: questions on rna-seq data analysis
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