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came up while discussing multiplicative combinations of single cell paired end polyA RNAseq, etc. on 14 May 2018
needs more discussion
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Hello,
I have received the following error while running the provided test script
`Traceback (most recent call last):
File "/remote/idiap.svm/group.genomics/zmxu/PolyAMiner-Bulk/Demo/../PolyA…
zmx21 updated
3 months ago
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Hi,
I am trying to run Bayesembler on a tophat2 (2.0.8) generated file from human K562 whole cell polya+
RNAseq (dUTP protocol):
https://www.encodeproject.org/files/ENCFF412EYU/@@download/ENCFF412EYU…
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The dataset types in the gEAR portal are nice and tidy:
```
mysql> select dtype, count(dtype) from dataset group by dtype;
+-----------------------+--------------+
| dtype | coun…
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I have a stats file that looks as below:
`{
"stats": {
"artefactStats": {
"RTP-RTP": 36655,
"TSO-TSO": 413310,
"no artefact": 1316939
…
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Thanks @marcelm for maintaining such a useful tool!
Regarding the relatively new poly-A trimming feature - would it be possible to toggle strandedness?
By default you consider R1 to have the po…
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General description of the project:
- MinION sequencing
- maintenance host vs. incidental hosts
- comparative study
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Running expHTS preprocess with polyA trimming, output fastq have invalid lines. See attachment with two examples of this.
Monica Britton
[invalid_fastq_lines.txt](https://github.com/msettles/expHTS/…
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Hi,I'm running the module how to estimate poly(A) tail lengths from nanopore native RNA reads, and I've got the result file, but I don't understand the result file right now, I think this command line…
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Hi Shuangshuang,
Considering a gene can produce multiple transcripts, is there a method to obtain a transcript counting matrix instead of a gene-based one during data preprocessing?
Thank you!