User: lzsph

gravatar for lzsph
lzsph70
Reputation:
70
Status:
New User
Location:
Last seen:
6 years, 3 months ago
Joined:
7 years, 4 months ago
Email:
l****@yahoo.com

about me

Posts by lzsph

<prev • 20 results • page 1 of 2 • next >
0
votes
1
answer
3.1k
views
1
answers
Comment: C: [Solved] Exception: Bio::Root::Exception When Using Sma3S For Annotation
... Hi Evan, It works well now. Thanks! ...
written 6.4 years ago by lzsph70
1
vote
1
answer
3.1k
views
1
answer
[Solved] Exception: Bio::Root::Exception When Using Sma3S For Annotation
... Hey guys, Recently, I did some annotation of my de novo assembled transcriptome in a non-model plant RNA-seq project, using Sma3s. I installed the softwares and modules required according to the documentation here. Version: Perl (v5.12.4), BioPerl (1.006901, checked the version using the co ...
annotation bioperl written 6.4 years ago by lzsph70 • updated 2.1 years ago by Biostar ♦♦ 20
0
votes
1
answer
4.7k
views
1
answers
Comment: C: De Genes And Isoforms?
... Thank you Assa! DAVID does much faster than Blast2GO and REVIGO's visualization looks great. I'll give it a try. My DE list tagged with interior tags such as comp11_c0 that supplied with Trinity rather than gene IDs/accessions. I should prepare a gene list with accessions and then upload it to D ...
written 6.6 years ago by lzsph70
1
vote
1
answer
4.7k
views
5 follow
1
answer
De Genes And Isoforms?
... Hey guys, We de novo assembly our transcriptome using Trinity, then aligned and quantified using RSEM's Perl script run_RSEM_align_n_estimate.pl supplied with Trinity. This resulted two results, say RSEM.isoforms.results and RSEM.genes.results. We performed differential gene expression analysis usi ...
ngs differential-expression rna-seq written 6.6 years ago by lzsph70 • updated 2.6 years ago by Biostar ♦♦ 20
1
vote
2
answers
2.9k
views
2
answers
Answer: A: Creating Go Chart Using Available Go Ids
... Maybe you should use blast2go, but you may have to format your data shown above into the .annot format required by blast2go and import it to b2g. I used blast2go to generate the GO pie chart a little earlier. ...
written 6.6 years ago by lzsph70
0
votes
1
answer
5.0k
views
1
answers
Comment: C: Command Or Script To Generate An Annotation File For Blast2Go
... Hi Whetting, thanks again. It's perfect!!! ...
written 6.8 years ago by lzsph70
0
votes
1
answer
5.0k
views
1
answers
Comment: C: Command Or Script To Generate An Annotation File For Blast2Go
... Hi Whetting, Awesome. By the way, how to keep one protein name in each set? Like this below. comp1000113c0seq1 GO:0043531 Cc-nbs resistance protein comp1000113c0seq1 GO:0005524 comp1000113c0seq1 GO:0017111 comp1000113c0seq1 GO:0006952 Thank you very much! Regards, Lzsph ...
written 6.8 years ago by lzsph70
3
votes
1
answer
5.0k
views
1
answer
Command Or Script To Generate An Annotation File For Blast2Go
... Dear all, We have got RNA-Seq of a plant without a reference genome, so we de novo assembled its transcriptome using Trinity. Now we have an annotation file of this transcriptome. I want to generate GO (Gene Ontology) functional classification using Blast2GO. But re-mapping my Blast XML results in ...
go written 6.8 years ago by lzsph70 • updated 6.8 years ago by Whetting1.5k
0
votes
2
answers
3.2k
views
2
answers
Comment: C: Annotating Rna-Seq Data Using A Reference Genome.
... OK, Ilia, I'll get it a try. Thank you! Regards,lzsph ...
written 6.8 years ago by lzsph70
0
votes
2
answers
3.2k
views
2
answers
Comment: C: Annotating Rna-Seq Data Using A Reference Genome.
... Hi Ilia, Thank you very much. I have a query file contains ~200,000 sequences with various lengths, and the tabular output of blastx also contains many sequences with different lengths, is it possible to set only one alignment length value in the command "...($4>=yourlength)"? If I was wrong, ...
written 6.8 years ago by lzsph70

Latest awards to lzsph

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1036 users visited in the last hour