User: Tom
Tom • 530
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... Would you recommend classifying reads with kraken and then making a transcript assembly from the ones that interest me? Or would i assemble transcripts from all reads and then try to classify those transcripts? ...
written 6 weeks ago by
Tom • 530
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... Thank you for the answer. Maybe that is the best approach. I am building the kraken database right now. Will report back on how well that works out. ...
written 7 weeks ago by
Tom • 530
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... Hi everyone,
I have several mRNA-Seq datasets from mixed bacterial communties, so metatranscriptome data. I am only interested in a single species in these communties and would like to find out which transcripts in the community belong to this species.
My approach so far was to do a transcriptome ...
written 7 weeks ago by
Tom • 530
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... Should anybody still stumble upon this thread (like i just did):
In my case the errors were caused by features where the start position was greater than the end position in the .GTF file. I assume this happens because i'm looking at circular bacterial chromosomes and the assemblies start somewhere ...
written 5 months ago by
Tom • 530
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Comment:
C: Using RPK counts as DESeq2 input
... I know this thread is old, but since i myself often get information from older biostars-threads:
I am pretty sure you are messing up the statistics by doing that. Let's say we are looking at a particular gene with a count of 1000 in condition A and a count of 3000 in condition B. If we divide these ...
written 6 months ago by
Tom • 530
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... I'm new to RNAseq and have yet to fully understand the statistics behind deseq myself. But i could image that the prerequisite assumptions about RNA-datasets might not hold true for your situation (e.g. are you certain that more than 50% of species have identical abundance between conditions?).
Als ...
written 6 months ago by
Tom • 530
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... I am relatively new to RNAseq and i don't yet fully understand the statistics involved in differential expression (DE) analysis. I have read quite a few publications where the DESeq2 package is used for DE-analysis of metatranscriptome datasets.
What confuses me in this context is the shrinkage est ...
written 6 months ago by
Tom • 530
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... Hi Sehrish!
There seems to be an issue with the `InitialWorkDirRequirement`. You cannot pass a string to the `listings` field. It has to be either files, directories or dirents.
We can, however, build a `dirent` for an empty directory named after the `input_folder` string:
requirements:
...
written 10 months ago by
Tom • 530
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... I'm not able to test this right now, but my guess would be: Everything works as intended CWL-wise, meaning a symlink to the directory is created in the temporary directory where step two is carried out. Calling `ls` with the `-l `flag causes it to not follow symlinks, so nothing is listed.
Best reg ...
written 11 months ago by
Tom • 530
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Comment:
C: Input specific output filenames
... Hi again!
`inputs.seqfile` is an array. While the elements in the array probably have a basename, the array itself does not. Would taking the name of the first file in the array be sufficient for your purposes?
inputs.seqfile[0].basename
Also note that `basename` includes the file extension, ...
written 11 months ago by
Tom • 530
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