5
votes
Accepted
Calculating most abundant transcript from RNA-Seq data
Transcript abundance quantification is a tricky topic since a read often could belong to several transcripts, so any "count" is a best guess as to which transcript it actually originates ...
4
votes
Accepted
How do I increase the sensitivity of Salmon Alevin?
So, I think there are a few potential options here. Alevin is using selective-alignment internally to determine the mappings for the reads. So, even if you have a k-mer supporting the mapping, if ...
- 482
4
votes
Download multiple fastq files using fastq-dump
A sample code is given in the salmon documentation as follows. Source
...
- 86
4
votes
Accepted
Salmon output: transcripts quantified with zero reads support
All transcripts should always be returned in the output, whether there's evidence supporting their expression or not. This is for the sake of simple convenience, since typically one would be merging ...
- 19.8k
2
votes
Accepted
tx2gene file for tximport issue
The solution was to use a different library as I expected. It should be library(TxDb.Hsapiens.UCSC.hg19.ensGene). And also, as specified in the question, to remove ...
- 2,578
2
votes
Why are my kallisto and salmon results differing so much just for lncRNA transcripts?
There has been a detailed comparison of kallisto and salmon for lncRNA transcripts by Zheng et al https://www.biorxiv.org/content/biorxiv/early/2018/01/09/241869.full.pdf
It shows them to be near ...
- 21
2
votes
RNA-seq analysis of mixed viral/host reads with salmon
You provide Salmon with a transcriptome fasta... so merging the human transcriptome with the pox virus genome fasta file should work. You don't mention that in your post but the viral genome should ...
- 1,613
2
votes
lower mapping rates in salmon v0.13 compared to previous versions
[Most likely answer based on comments attached to the question]
Hi Courtney, We've looked into the data and identified the source of the different mapping rates. Specifically, the cause is discordant ...
2
votes
Snakemake MissingRuleException
You're not using wildcards the way snakemake is equipped to work with them. See:
FAQs such as https://snakemake.readthedocs.io/en/stable/project_info/faq.html#how-do-i-run-my-rule-on-all-files-of-a-...
- 2,498
1
vote
Accepted
After running nf-core, is there a way to map a gene_id to a specific gene's DNA sequence?
fishing out tp53 RNA-Seq reads
go to NCBI Taxonomy Browser
put Anas platyrhynchos as a search term
click on Anas platyrhynchos
...
- 398
1
vote
Bulk RNA-Seq Read Length Normalization across different samples
The simplest thing to do is to trim the 150 bp fasts so that they are 100 long. I don't think there is an easy way to correct for the fact that the 150 bp long reads will have a higher unambiguous ...
- 2,061
1
vote
Download multiple fastq files using fastq-dump
Make a list.txt file containing a single column of SRA numbers to download.
then:
for i in $(cat list.txt); do echo $i; date; fasterq-dump -S $i; done
It works well ...
- 221
1
vote
Accepted
Where to get '--fldMean' and '--fldSD' for single-end Salmon run
From looking at the salmon documentation here, it is correct that both of these are essential for single end experiments:
Since the empirical fragment length distribution cannot be estimated from ...
- 1,069
1
vote
tx2gene file for tximport issue
Do your ids in the expression file (from gencode) match up with the gene IDs in the transcript file (from UCSC?) I'm willing to bet that they don't. Stay consistent throughout your process. Either ...
- 530
1
vote
Accepted
Exception : [Failed to read 8 bytes from input stream! Read 0] salmon quant was invoked improperly
The issue was caused by the corrupted input .fastq files that were damaged somehow upon uploading them from the local machine. We figured it out by ...
- 2,578
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