User: ugurcabuk

gravatar for ugurcabuk
ugurcabuk110
Reputation:
110
Status:
Trusted
Location:
Turkey
Last seen:
3 hours ago
Joined:
2 years, 2 months ago
Email:
u**********@gmail.com

Posts by ugurcabuk

<prev • 35 results • page 1 of 4 • next >
0
votes
1
answer
388
views
1
answers
Comment: A: Comparing SPAdes assemblies to each other?
... I think, [Quast][1] work for you. All you need to do is to check the parameters. It has got alignment parameter. [1]: http://bioinf.spbau.ru/quast ...
written 1 day ago by ugurcabuk110
0
votes
0
answers
89
views
0
answers
Comment: C: Why one genome assembly is more fragmented than others?
... I don't know exactly what the reason is but did you assessment your all assemblies using BUSCO tool ? Maybe in the genome assembly you mentioned contains contamination or missing in your raw data ? ...
written 6 days ago by ugurcabuk110
0
votes
1
answer
68
views
1
answers
Answer: A: Display bootstraps on tree RAxML-NG
... check the link I answered kind of the same question in the forum https://www.biostars.org/p/446023/#446027 ...
written 6 days ago by ugurcabuk110
0
votes
0
answers
78
views
0
answers
Comment: C: Find transcripts of one species in RNA-assembly
... I would recommned you that, at least my approach, firstly classify the reads using kraken and then assembled them. After classifying them, whichever species you want to extract from the reads can be filtered based on taxonomy id in the file. ...
written 6 days ago by ugurcabuk110
2
votes
1
answer
89
views
1
answers
Answer: A: reorder contigs into scaffold?
... What kind of organism ? Please, give more information. However, There are some tools to make it. [Contiguator][1] [ABACAS][2] [Mauve][3] If it is bacteria, the article, [Approaches for in silico finishing of microbial genome sequences][4], can give you some ideas [1]: http://contiguator.sou ...
written 10 days ago by ugurcabuk110
0
votes
1
answer
102
views
1
answers
Comment: C: Is the ssGSEA enrichment score affected by other samples in the analysis group?
... It is interesting.. I haven't never seen such a issue since I have run it. But you can also use the other packages for single sample analysis. I would recommend you to try [GSVA][1] and [Singscore][2] [1]: https://bioconductor.org/packages/release/bioc/html/GSVA.html [2]: https://bioconductor. ...
written 13 days ago by ugurcabuk110
1
vote
0
answers
78
views
0
answers
Comment: C: Find transcripts of one species in RNA-assembly
... Did you try to use [KRAKEN][1] to find them ? [1]: https://ccb.jhu.edu/software/kraken/ ...
written 13 days ago by ugurcabuk110
1
vote
1
answer
73
views
1
answers
Answer: A: RAxML generate best tree from 500 bootstrap trees
... Check the `-f` parameter in the manual I attached. It may be `-f a` [RAxML Manual][1] [1]: https://cme.h-its.org/exelixis/resource/download/NewManual.pdf ...
written 13 days ago by ugurcabuk110
0
votes
0
answers
106
views
0
answers
Comment: C: Constructing reference-based draft genome
... Thanks for quick reply, genomax. Right ! Maybe the safest approach is that get long reads to polish it. Unfortunately in my situation, I have to apply only bioinformatics approaches. I evaluated my assembly using BUSCOs and I got good results over 99%. Can you explain creating a net library a bit? ...
written 17 days ago by ugurcabuk110
1
vote
0
answers
106
views
0
answers
Constructing reference-based draft genome
... Hi all, I have been dealing for a while about getting draft genome of bacteria. I have chosen a closely related bacteria to make reorder contigs and concatenate them using ABACAS. This closely related bacteria was selected based on phylogenetic tree result. However, the problem is that genome size ...
genome assembly next-gen written 17 days ago by ugurcabuk110

Latest awards to ugurcabuk

Popular Question 9 days ago, created a question with more than 1,000 views. For GSVA and SSGSEA for RNA-Seq TPM data
Scholar 10 days ago, created an answer that has been accepted. For A: How to filter BLAST results by query coverage? How to analyze large BLAST output
Scholar 28 days ago, created an answer that has been accepted. For A: How to filter BLAST results by query coverage? How to analyze large BLAST output
Teacher 28 days ago, created an answer with at least 3 up-votes. For A: How to filter BLAST results by query coverage? How to analyze large BLAST output

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1401 users visited in the last hour