fr-firststrand or not ?

IGV SNAPSHOT :[2] http://postimg.org/image/4xjcmzorz/

Hello everyone, Quick question, just to confirm, is this fr-firststrand ?

Single - end reads , all mapped to the opposite direction of the gene.

Thanks

rna-seq strand specific single end

• 1,902 views • link

updated 10.3 years ago by Biostar

• written 10.4 years ago by siddharth.sethi5

See Devon's answer: consistent problem of strand-specific information between TopHat/RSeQC/picard

• 0 views • link

written 10.4 years ago by GenoMax

0 answers

No answers yet.

More posts like this

Single-end strand specific Rna-Seq: Which strand that the reads from.
written 3.0 years ago by Chilly •

Hi everyone, I have searched online for a long time, but there is still no authoritative answer to this question (for **single-end sequencing**). So, I …
Read coverage shows a difference in IGV
written 3.9 years ago by jkim •

Hello, This is my bam file in IGV. There are way more reads mapped to the region 2 in the panel displaying reads. On the …
RSeQC Output from infer_experiment.py - what does it mean?
written 8.5 years ago by JJ

Hi all, Can someone help me understand the RSeQC Output from infer_experiment.py? So this is the output: This is PairEnd Data Fraction of reads failed …
Converting PE to SE
written 8.8 years ago by Picasa

Hello, I have RNAseq paired end in fr-firststrand (as described here http://chipster.csc.fi/manual/library-type-summary.html). I have also RNA reads in single end (reverse orientation). I need to …
Some basic question on quantification of RNA-seq mapped reads
written 9.0 years ago by Hamid •

Hello everyone, I'm trying to use stringtie to quantify some previously mapped RNA-seq reads. And I have some basic questions. I appreciate if someone explains …
How can all BWA alignment get wrong mapping location?
written 10.2 years ago by tiago211287

I mapped using bwa, 2 paired end sequences from exome sequencing using this command: bwa mem -t 10 -M -R '@RG\tID:group1\tSM:sample1\tPL:illumina\tLB:lib1\tPU:unit1' h19_index_bwa/h19 MM160301JR_1.fastq MM160301JR_2.fastq > …
Plotting Density Of Reads On Chromosomes
written 11.8 years ago by scszsc •

I want to plot a picture like this: [![< image "20141014104516" not found >][1]][2] Short reads mapped to genome with bowtie etc. And then, Plot …
Count 5'End Mapped To A Specific Genomic Position
written 12.9 years ago by ifreecell

I got several <a href='http://samtools.sourceforge.net/SAM1.pdf'>SAM</a>/BAM files, and I am interested in 5'ends of the mapped reads. Is there any tools or scripts to count how …
Rpkm Calculation For Genes
written 13.8 years ago by siddharth.sethi5

Hi everyone I understand the RPKM fomula is as follows: C = Number of reads mapped to a gene N = Total mapped reads in …
Cufflinks And Solid 5500 Rnaseq Bam Files
written 14.0 years ago by Ashutosh Pandey

Hello everyone, I have RNAseq data generated on SOLiD 5500 machine. I used Lifescope mapping tool to align the reads against the reference genome and …