Question: Mapping both PE reads and Single-end reads into transcriptome
0
gravatar for pbigbig
2.0 years ago by
pbigbig210
United States
pbigbig210 wrote:

Hi everybody,

I built several de novo transcriptomes from non-model organism without genome reference by Trinity. Sequencing libraries were prepared with stranded method (dUTP), therefore I only used paired-end reads with RF SS_lib_type parameter in Trinity for assembling. However, earlier preprocessing steps retained ~20% amount of data as singletons (reads that lost their pair due to filtering), I really want to use this data as single-end reads to simultaneously map to de novo transcriptome together with PE reads. My final purpose is performing Differential expression analysis of coding mRNA.

Could you please suggest any tools for mapping both SE and PE reads to transcriptome, is BWA a good choice? Furthermore, does strand information have any benefit in case of mapping reads on transcriptome? (since we do not know reference genome sequence)

Thank you very much in advance !

ADD COMMENTlink written 2.0 years ago by pbigbig210

You can use the Trinity pipeline to align your SE/PE reads back to the transcriptome you assembled, which used Bowtie for alignment. The subsequent BAM files will be used to quantify abundance estimates.

ADD REPLYlink written 2.0 years ago by st.ph.n2.5k
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: 781 users visited in the last hour