search

trinityrnaseq / trinityrnaseq

Trinity RNA-Seq de novo transcriptome assembly
BSD 3-Clause "New" or "Revised" License
835 stars 320 forks source link

De novo assembly for non-reference genome #529

Closed mirzaabidpp closed 6 years ago

mirzaabidpp commented 6 years ago

Hi, I am working on RNA-seq (mRNA) PE data 150x2 of microbial communities. I read a paper in which they used trinity to assemble mRNA reads. So I tried to use it for my data as well with the following command

.../Trinity --seqType fq --left 3B_1.fq --right 3B_2.fq --CPU 30 --max_memory 100G

As a result, I obtained other files and FASTA file named both.fa. I thought it might be paired now hence checked stats by using ..../trinityrnaseq-Trinity-v2.6.6/util/TrinityStats.pl both.fa but the contig size remained the same for N10-N50 =150 it means that reads are not joined together. I need your valuable suggestions to solve this problem as I am newbie in bioinformatics

brianjohnhaas commented 6 years ago

Hi,

the both.fa file is just the concatenated reads that are used by Trinity for assembly. There should be a Trinity.fasta file containing the assembled transcripts if the process finishes successfully.

best,

~b

On Thu, Jul 26, 2018 at 1:18 PM abid notifications@github.com wrote:

Hi, I am working on RNA-seq (mRNA) PE data 150x2 of microbial communities. I read a paper in which they used trinity to assemble mRNA reads. So I tried to use it for my data as well with the following command

.../Trinity --seqType fq --left 3B_1.fq --right 3B_2.fq --CPU 30 --max_memory 100G

As a result, I obtained other files and FASTA file named both.fa. I thought it might be paired now hence checked stats by using ..../trinityrnaseq-Trinity-v2.6.6/util/TrinityStats.pl both.fa but the contig size remained the same for N10-N50 =150 it means that reads are not joined together. I need your valuable suggestions to solve this problem as I am newbie in bioinformatics

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/trinityrnaseq/trinityrnaseq/issues/529, or mute the thread https://github.com/notifications/unsubscribe-auth/AHMVX9dhxdPnm7Gjx2j1BZIkELyjWpH7ks5uKfnYgaJpZM4ViOwH .

--

Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas