Question: Cufflinks And Solid 5500 Rnaseq Bam Files
0
gravatar for Ashutosh Pandey
6.7 years ago by
Philadelphia
Ashutosh Pandey11k wrote:

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 got bam files. Now, I want to use Cufflinks for the further analysis. My RNAseq data is 50 bp fragment reads (single/unpaired) and I am not sure which library type I should use. Here are the options in Cufflinks:

Library Type

fr-unstranded (default) Standard Illumina Reads from the left-most end of the fragment (in transcript coordinates) map to the transcript strand, and the right-most end maps to the opposite strand.

fr-firststrand dUTP, NSR, NNSR Same as above except we enforce the rule that the right-most end of the fragment (in transcript coordinates) is the first sequenced (or only sequenced for single-end reads). Equivalently, it is assumed that only the strand generated during first strand synthesis is sequenced.

fr-secondstrand Directional Illumina (Ligation), Standard SOLiD Same as above except we enforce the rule that the left-most end of the fragment (in transcript coordinates) is the first sequenced (or only sequenced for single-end reads). Equivalently, it is assumed that only the strand generated during second strand synthesis is sequenced.

I assume I should be using the fr-secondstrand. But i just want to make sure?

Thanks a lot.

cufflinks solid • 1.9k views
ADD COMMENTlink modified 5.2 years ago by Biostar ♦♦ 20 • written 6.7 years ago by Ashutosh Pandey11k
0
gravatar for JC
6.7 years ago by
JC7.7k
Mexico
JC7.7k wrote:

because your data is single-ends you don't need to define the --library-type option, that's for paired-end reads.

ADD COMMENTlink modified 6.7 years ago • written 6.7 years ago by JC7.7k
1

That is true. However SOLiD reads retain strandness throughout the library prep. Does cufflinks assume unstranded reads as default in single read assemblies? I wonder if defining a library type will allow Cufflinks to take advantage of that strandness even in single read assemblies.

ADD REPLYlink written 6.7 years ago by Damian Kao15k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1052 users visited in the last hour