Salmon number of burn-in fragments warning
I am very new to salmon so I'm sorry if this is a silly question but I am trying to map some RNA-seq data to a seabass Transcriptome. I've made an index and am making to it but I get a very low mapping rate. I've been able to improve it but it is still 16%.
There is this warning:
Only 2807463 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.
Is this something I should be concerned about and how should I address it?
Thanks in advance!!
• 1,500 views
•
link
updated
by
h.mon
•
written
by
bioinfo_cat •
•
written
by
bioinfo_cat •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
how to interpret very short effective length in Salmon output
written by hans •
-
Salmon indexing directory missing files?
written by bioinfo_cat •
-
Confusion about Salmon library type
written by tianshenbio
-
Where is the (hg19) reference data for transcript isoforms' relative abundances for each gene?
written by Joel Wallenius
-
Can Salmon's quantification method accommodate concatenated reads of varying length (from independe…
written by c_dampier
-
Big differences between mappings computed by Salmon and quantification
written by KDA •
-
How should effective lengths returned by Salmon be collapsed for Differential Expression?
written by arf1389 •
-
salmon, kallisto psuedoaligners are failing to process
written by dr.prasad.bvls •
-
Having trouble with biomaRt, getBM and chromosome_end
written by R.Blues
-
How To Represent Restriction Sites In Gff3
written by Daniel Standage
