Skip to main content
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 ...
Bastian Schiffthaler's user avatar
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 ...
nomad's user avatar
  • 482
4 votes

Download multiple fastq files using fastq-dump

A sample code is given in the salmon documentation as follows. Source ...
Balan's user avatar
  • 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 ...
Devon Ryan's user avatar
  • 19.7k
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 ...
Nikita Vlasenko's user avatar
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 ...
Lior Pachter's user avatar
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 ...
story's user avatar
  • 1,603
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-...
Ram RS's user avatar
  • 2,454
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 ...
darked89's user avatar
  • 388
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 ...
swbarnes2's user avatar
  • 1,971
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 ...
Stuber's user avatar
  • 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 ...
Matt Bashton's user avatar
  • 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 ...
chrisamiller's user avatar
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 ...
Nikita Vlasenko's user avatar

Only top scored, non community-wiki answers of a minimum length are eligible