User: Tom_L

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Tom_L320
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Posts by Tom_L

<prev • 38 results • page 1 of 4 • next >
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Comment: C: RNA-seq data from human tumors in mice (PDTX)
... Thank you for clarifying these points. This makes sense to me. ...
written 20 months ago by Tom_L320
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Comment: C: RNA-seq data from human tumors in mice (PDTX)
... Thank you for you reply. This method (and some others) looks a good tool for WES or WGS because most tools are designed to accurately identified actual mutations (or somatic SVN) from mouse SNP. Some of them even try to detect structural variations! However, as highlighted in fig 6b, the transcripto ...
written 21 months ago by Tom_L320
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RNA-seq data from human tumors in mice (PDTX)
... Hello, I'm working in a cancer center where we use PDTX (Patient-Derived Tumor Xenograft) so the principle is to graft human tumors in mice. We recently reached a dead-end as we wanted to performed some RNA-seq (75bp; paired-ends) on these tumors. The problem is that there always is a cellular cont ...
mouse rna-seq human written 21 months ago by Tom_L320 • updated 21 months ago by breckuh30
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Comment: C: Combining multiple files into a single text file in R
... This is not bioinformatics, just text formatting. However, it's not different from recurrent questions about BED or SAM formatting either. What's the limit? ...
written 2.1 years ago by Tom_L320
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Comment: C: Combining multiple files into a single text file in R
... That is weird, I frequently use "*do.call*" with input similar to the one you show in the picture. "*rbind*" should definitely works as you just want to append file contents. If you have a problems with columns/row transition, can you try a matrix transposition : "*t()*"? ...
written 2.1 years ago by Tom_L320
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Comment: C: Combining multiple files into a single text file in R
... How about "*dataFiles_converted=do.call(rbind,dataFiles)*"? ...
written 2.1 years ago by Tom_L320
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Comment: C: How to align mouse transcriptome data using bowtie2?
... You can either concatenate all chromosomes into a single file or download a single file that directly contains all chromosomes. Usually, software work with a single file as it is simpler to handle. See here for mm10 genome version: http://hgdownload.cse.ucsc.edu/goldenPath/mm10/bigZips/ ...
written 2.5 years ago by Tom_L320
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Comment: C: Trinity: how to avoid out of memory error in butterfly
... Are you sure that the problem comes from how much RAM is required? I believe you ask too many cores to your server: *unable to create new native thread* (https://plumbr.eu/outofmemoryerror/unable-to-create-new-native-thread). Most Trinity problems can be resolved by lowering CPU requirement (16-32 c ...
written 2.9 years ago by Tom_L320
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Answer: C: Human transcription download
... I recommend you to use the information available in the [Table Browser from UCSC][1]. Pick your genome version (hg19 or hg38), choose your annotations (Ensembl, RefSeq, etc.) and get the GTF output format. RefSeq is a good starting point. If you need a transcriptome fasta file, you can use the gtf_t ...
written 2.9 years ago by Tom_L320
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Comment: C: How to statistically compare two unit vectors?
... How about computing the [Wilcoxon's RST][1] ([Shapiro–Wilk][2] test is significant for nw so it is not normally distributed)? I didn't understand if your data is paired or not. If yes, use the [Wilcoxon's signed-RST][3]. [1]: https://en.wikipedia.org/wiki/Mann%E2%80%93Whitney_U_test [2]: http ...
written 2.9 years ago by Tom_L320

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Popular Question 24 months ago, created a question with more than 1,000 views. For Survival analyses: how to compare multiple groups?
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