This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Why only reverse fatsq file is used for mapping step in single cell RNA sequencing analysis?

Dear all,

I am following a tutorial to do ScRNA-Seq analysis.

In the mapping step it has been advised to use the reverse strand, however I don't understand the logic behind this.

Can anyone explain to me why we should only use the reverse file for mapping?

Regards

scrna-seq
• 1,678 views • link
updated by Ram Ram • written by nazaninhoseinkhan nazaninhoseinkhan

1 answer

R1 is bar codes+UMI

• 0 views • link
written by cpad0112 cpad0112

Thank you so much

So it means that both reverse and forward strands have been merged in R2?

• 0 views • link
written by nazaninhoseinkhan nazaninhoseinkhan

There is no merging.

• 0 views • link
written by cpad0112 cpad0112

Log in to answer this question.

More posts like this
  • Understanding STARsolo --soloStrand values and 10X scRNA-seq library structure
    written by mk mk
    #### Background: [These github docs][1] for STARsolo specify `--soloStrand=Forward` for all 3' 10X scRNA-seq and `--soloStrand=Reverse` for all 5' 10X scRNA-seq libraries. However, Alex Dobin …
  • DEGs vs WGCNA: What am I really looking at?
    written by christiantd • christiantd
    Hi all, I have previously performed DEG-analysis using DESeq2 on a dataset that has 2 groups (let's say group A and group B) and 6 …
  • Housekeeping genes scRNA seq
    written by bioinformatics • bioinformatics
    Hello, I am trying to follow this workflow for scRNA seq analysis. https://broadinstitute.github.io/2020_scWorkshop/data-wrangling-scrnaseq.html#filtering-low-quality-cells I have loaded the data and computed the percentage of mitochondrial genes …
  • edgeR, Pseudobulk scRNA-seq
    written by bioinformatics.girl • bioinformatics.girl
    Hello-- I am a bit familiar with the preface of pseudobulk differentiall expression analysis, however cannot find succinct tutorials for newbies concerning edgeR for scRNA-seq. …
  • Complexity of gene expression in scRNA-seq data
    written by kinalimeric • kinalimeric
    Dear all, I am following this tutorial which is very understandable for single-cell analysis. However, I am confused about only one concept in here which …
  • miRNA-mRNA correlation data analysis
    written by rezaeir75 • rezaeir75
    I'm a wet lab Molecular Biologist who has experience with programming in Python and R, and I also know how to use bash. However, I'm …
  • RNA seq stranded
    written by ASid • ASid
    HI everybody. I am trying to understand a concept in RNA seq analysis if somebody could help. As far as i understand, in a stranded …
  • effective length of query in blast
    written by nazaninhoseinkhan nazaninhoseinkhan
    <p>Dear all,</p> <p>I don&#39;t understand the meaning of effective length of query in Blast which is used in calculation of e-value.</p> <p>Can anyone explain it …
  • Genbank file format is wrong?
    written by eddie.im eddie.im
    Hello, I'm having a hard time to understand the logic behind the Genbank file format. In special about the "complement" feature, which doesn't seems to …
  • The Meaning Of "Seq Being Reverse Complemented" In Sam Format
    written by Pascal Pascal
    <p>Hi</p> <p>After reading the <a href='http://www.google.es/url?sa=t&amp;rct=j&amp;q=sam%20format&amp;source=web&amp;cd=1&amp;ved=0CBsQFjAA&amp;url=http%3A%2F%2Fsamtools.sourceforge.net%2FSAM1.pdf&amp;ei=qMvETozfNZCu8QPCj5XqCg&amp;usg=AFQjCNFkMtvEi6LeiKgpxQGtHTlqWKw2yw&amp;sig2=XBPQQA8wfR9913zR14Y1mQ'>SAM specs</a> it is still not very clear what is the meaning of these two fields in the FLAG:</p> <ul> …