User: Tom

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Tom530
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Posts by Tom

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Comment: C: Find transcripts of one species in RNA-assembly
... 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 11 weeks ago by Tom530
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Comment: C: Find transcripts of one species in RNA-assembly
... 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 12 weeks ago by Tom530
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Find transcripts of one species in RNA-assembly
... 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 ...
metagenome rna-seq blast transcriptome written 12 weeks ago by Tom530
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Answer: A: featureCount not processing reads
... 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 6 months ago by Tom530
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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 7 months ago by Tom530
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Comment: C: Can I use deseq on non transcriptome data?
... 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 7 months ago by Tom530
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Is DESeq2 analysis valid for Metatranscriptomics?
... 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 ...
metatranscriptomics deseq2 rna-seq written 7 months ago by Tom530
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Answer: A: CWL: Using the "EnvVarRequirement" to pass an environment variable to a script
... 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 11 months ago by Tom530
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Answer: A: Missing CWL files in a Directory when passed as input
... 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 12 months ago by Tom530
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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 12 months ago by Tom530

Latest awards to Tom

Voter 12 weeks ago, voted more than 100 times.
Popular Question 7 months ago, created a question with more than 1,000 views. For CommandLineTool doesn't finish
Scholar 12 months ago, created an answer that has been accepted. For A: CWL to write into for writing lines one from one file to new file
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: samtools sort: failed to create temporary file "/BOredq/NA12878.sorted.bam.tmp.0
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: samtools sort: failed to create temporary file "/BOredq/NA12878.sorted.bam.tmp.0
Scholar 13 months ago, created an answer that has been accepted. For A: CWL to write into for writing lines one from one file to new file
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: samtools sort: failed to create temporary file "/BOredq/NA12878.sorted.bam.tmp.0
Scholar 13 months ago, created an answer that has been accepted. For A: CWL to write into for writing lines one from one file to new file
Scholar 15 months ago, created an answer that has been accepted. For A: CWL to write into for writing lines one from one file to new file
Scholar 16 months ago, created an answer that has been accepted. For A: CWL to write into for writing lines one from one file to new file
Scholar 19 months ago, created an answer that has been accepted. For A: CWL to write into for writing lines one from one file to new file
Scholar 19 months ago, created an answer that has been accepted. For A: CWL to write into for writing lines one from one file to new file
Scholar 19 months ago, created an answer that has been accepted. For A: CWL to write into for writing lines one from one file to new file
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Scholar 19 months ago, created an answer that has been accepted. For A: CWL to write into for writing lines one from one file to new file
Scholar 19 months ago, created an answer that has been accepted. For A: CWL to write into for writing lines one from one file to new file
Student 2.3 years ago, asked a question with at least 3 up-votes. For CommandLineTool doesn't finish

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