Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
Pre-processing/QC of sequencing data Q's Rookie General 1 06-22-2017 01:02 AM
ChIP-seq library pre-processing BatSeqs Bioinformatics 2 10-02-2014 02:06 AM
Processing SOLiD data from SRA using Tophat Helical SOLiD 2 07-14-2014 10:23 AM
Extent of reduction during pre-processing cerebralrust Bioinformatics 4 05-01-2013 05:17 AM

Thread Tools
Old 08-24-2020, 02:34 AM   #1
Location: Bangkok, Thailand

Join Date: Apr 2015
Posts: 10
Unhappy Please help!! Completely new to pre-processing Drop-Seq SRA file from database

Dear all great helpers,

I'm completely new to Drop-seq analysis, and I do have no clue how to preprocess Drop-Seq data acquired from SRA database. For example, I have tried downloading and spiting SRR11014434 data file. Now I have two fastq files as follows: SRR11014434_1.fastq and SRR11014434_2.fastq.

I've started by learning from the Drop-seq cookbook ( As far as I understand the SRR11014434_2.fastq file contains data about the UMI and Cell barcode, while the SRR11014434_1.fastq file contains expression data of the cell.

Since the cookbook demonstrate step-by-step starting from raw read counts acquired from sequencer, I'm now totally confused with what I'm doing. Some of the very basic but critical questions are as follows:

1) Is the data already demultiplexed?
2) Am I supposed to align SRR11014434_2.fastq by STAR? What should I do after this step? The cookbook talked about merging mapped and unmapped BAM file, tagging exon/gene annotations. But I totally how am I suppose to do this without the unmapped bam file (All I could think about is trying to include unmaaped read the output sam file acquired from STAR using --outSAMunmapped Within option and use it as the merged file).

Please help me!!

TofuKaj is offline   Reply With Quote

database retrieve, drop-seq, pre-processing

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 09:14 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO