All Questions
Tagged with rna-alignment phylogenetics
9 questions
1
vote
1
answer
260
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What is the meaning of split read?
I want to use rna seq data to later perform functional tests on fusion genes.
so before that I need to filter the "best results" (of rnaseq) for deciding which candidates I actually want to ...
2
votes
1
answer
102
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Understanding ViennaRNA RNAdistance scoring table
I'm trying to compare the output of 2 different algorithms of RNA structure prediction
(my implementation of Nussinov vs RNA-mfold algorithm) using the RNAdistance algorithm that is part of ViennaRNA ...
- 141
1
vote
1
answer
50
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What is the best way to map/align my reads on a given genome?
I am frequently using a ballgown package for my rnaseq analysis, but recently I have had a new task to have my reads mapped on two different genomes to understand the level of alignment between the ...
0
votes
0
answers
59
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Best way to align to find inserted sequence
We have some RNA from knock-in mice, there are two different sequences we're looking for. We have aligned to the mouse genome using STAR but the sequence isn't there which isn't too surprising What is ...
- 95
3
votes
1
answer
475
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cDNA and alignment mapping
I am confused with RNA seq alignment. My understanding is that after Mature mRNA is isolated from the cell, it is then fragmented and using reverse transcriptase enzyme a cDNA copy is created which is ...
- 31
8
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1
answer
5k
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What are "split reads" and "intron clusters?"
I'm working through the example data set for LeafCutter and the documentation mentions "split reads":
This will cluster together the introns fond [sic] in the junc files listed
in test_juncfiles....
- 277
2
votes
1
answer
260
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Merging ssu-align alignments
ssu-align is an HMM-based MSA tool for ribosome's small subunit (SSU) sequences. It's bundled with three SSU models:
archaeal,
bacterial
eukaryotic
Approach Given a set of archaeal and ...
- 79
1
vote
1
answer
588
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Why is my STAR reference genome indexing aborting on my GNU/Linux server but not on my Mac OS X laptop?
I am running the following command to index my genome:
...
- 2,479
6
votes
3
answers
247
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Show presence of known mutation in RNA-seq data
We have RNA-seq fastq data from control (WT) patients and a patient with a point mutation at a known location in one gene.
I'd like to retrieve the reads aligning to that gene and show the presence of ...
- 2,644