unigenes not cluster together · Biostar

This is a test version of Biostars. For the public version, visit https://www.biostars.org.

unigenes not cluster together

Hi, I met a problem, I hava two samples,the two samples are the same species, they have a similarity of 90%,the two samples are assembled by trinity respectively, I got more than 60000, 50000 unigenes respectively. I used cd-hit to remove redundancy and tgicl to cluster unigenes. I got 90000 unigenes, most unigenes are not clustered. I blast two samples, the mapped result is 75%. Why most unigenes are not clustered?

assembly

• 1,744 views • link

updated 4.5 years ago by Ram

• written 10.5 years ago by songmm19900210 •

0 answers

No answers yet.

Log in to answer this question.

More posts like this

Differentially Expressed Unigenes (DEGs)
written 5.9 years ago by wes •

Dear All I came across the paper below and would like to apply the methods for my study. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5855742/ De Novo Assembly: High-quality clean reads …
De novo transcriptome assembly produce too many transcripts
written 7.5 years ago by 21afiq •

Hi, I just finished my transcriptome assembly using Trinity. However, the transcripts produced by trinity is too many (~300k transcripts) which is not normal for …
How reads are considered as mapped using samtools idxstats?
written 8.3 years ago by lakhujanivijay

I am trying to quantify the number of mapped reads on CDS regions using [samtools][1] idxstats. I want the number of reads mapped onto CDS …
CD-HIT can not complete remove redundant transcript
written 8.9 years ago by xioli2013 •

I tried to use CD-HIT-EST to remove redundancy in trinity de novo transcripts however I can still see redundant annotations, cd-hit-est -i trinity.fasta -o clstr_out …
Functional annotation pipeline
written 9.2 years ago by sbchua.1990 •

I have assembled a transcriptome using Trinity and clustering it using CD-hit with 0.95 threshold to reduce redundancy. For the clustered transcripts, I performed blastx …
How to cluster transcripts assembled using TRINITY into unigene after blast?
written 9.3 years ago by sbchua.1990 •

I have assembled a transcriptome using TRINITY with 100,000 transcripts. I have perform blastx against NR database (-outfmt 5). I want to remove redundancy in …
Is it right to merge different trinity transcript assembly of same plant ?
written 9.3 years ago by Mahendra Gaur •

Dear All, I have rna-seq data of 3 ginger sample of which are from different condition. I have assembled them using trinity tool, hence i …
Clustering of metabarcoding reads from many environmental samples
written 9.9 years ago by lvogel •

Hi, I've been using CD-HIT EST in the past to cluster sequences of COI from environmental samples. For my current project, however, there are over …
DNA sequence clustering tools
written 10.2 years ago by ngs101.com

Hi guys, I have about 300,000 sequences stored in a fasta file. I am trying to reduce the redundancy of these sequences. I used CD-HIT-EST …
Cluster proteins according to their domain architecture
written 11.4 years ago by dago

I have a list of proteins that I want to divide into homogeneous (in terms of potential similar function) clusters. As first approach I clustered …