Kallisto Single FastQ File Run
Hello, I am trying to run kallisto on this data set: https://www.ebi.ac.uk/ena/data/view/PRJNA292382
Since dataset is not paired kallisto gives this error, while running with --single flag: Error: fragment length mean and sd must be supplied for single-end reads using -l and -s
But I can't seem to find fragment length and mean and sd, how can I find this? I couldn't find it in the data set link as well.
• 1,644 views
•
link
written
by
osmanberkx0x •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Fragment size of published single end RNAseq data
written by kojima.1aki •
-
ENA fastq file shown as Paired-end but has 2 Run Accessions
written by Aaliya •
-
kallisto -s o error
written by 1_GOld •
-
mapping reads using kallisto - rna seq analysis
written by bioinformatics •
-
ENA fastq file shown as single-end but has 3 fastq files: X.fastq.gz X_1.fastq.gz X_2.fastq.gz
written by Mr Locuace
-
Running 3 FASTQ files for WGBS
written by Batu
-
Kallisto estimated sd and fragment length
written by bharata1803
-
Getting average fragment length for single end reads
written by Sreeraj Thamban
-
kallisto: strand-specific and fragment length calculation
written by user230613
-
Partial Codon Or Missing Stop Codon
written by Pappu
it’s best to determine this from a library quantification with an instrument such as an Agilent Bioanalyzer. Reference:https://pachterlab.github.io/kallisto/manual
Does one need to use this kind of tool to find fragment length mean and sd?
This is not a tool such as a software, it is a machine in the wetlab that can measure the size of the actual physical DNA fragment, so not possible obviously for downloaded data. For standard RNA-seq library prep kits such as TruSeq from Illumina or UltraII from NEB the actual insert size is typically around 100bp-250bp in my experience with a median of about 150bp. I would simply use 150 and a SD of 20 that probably gives a good proxy.