I'm new to RNA-seq and was wondering if there is a generally accepted minimum mapped percent (hg19)? Right now I seem to be getting around 60-70%. Thank you!
While the percentage can be much higher you have what you have. Are you using a splice-aware aligner? You can take a look at the reads that did not map by checking a few with blast @NCBI (unless you have already done this by "were checked for contamination").
Hey everyone, I've a rather technical question regarding assigned alignments percentage to human genome (GRCh38.p14) - I'm using Gencode v47 version along it's annotation. My …
Hi everyone, I've been working with rna-seq to analyze genome wide alternative splicing and was wondering if there are newer tools besides rMATS, SUPPA, and …
Hi all! Recently, we were given a choice between microRNA microarray OR small RNASeq for mouse. Upon further discussion, someone raised a question if mouse …
<p>Hi everyone, I'm mapping mRNA-seq data (single end, 40bp) of C.elegans to the cDNA reference (junction of exons) with bowtie, I'm a beginner for RNA-seq …
Where is your sample coming from? Is there a possibility of contamination? If yes, from which source.
The samples are from patients and were checked for contamination with none found. Thank you for your help!
While the percentage can be much higher you have what you have. Are you using a splice-aware aligner? You can take a look at the reads that did not map by checking a few with blast @NCBI (unless you have already done this by "were checked for contamination").