User: kristina.mahan
kristina.mahan • 100
- Reputation:
- 100
- Status:
- Trusted
- Location:
- Last seen:
- an hour ago
- Joined:
- 2 years, 1 month ago
- Email:
- k*************@gmail.com
Posts by kristina.mahan
<prev
• 62 results •
page 1 of 7 •
next >
0
votes
0
answers
70
views
0
answers
Comment:
C: Blobtools output files
... entire assembly is ~2000 contigs.
no-hits: 594 contigs
Bacteria: 252 contigs
Proteobacteria: 817 contigs
Haptista: 6 contigs
Chordata: 17 contigs
Euglena: 1 contig
Ascomycota: 3 contigs
Streptophyta: 7 contigs
Chlorobi: 1 contig
Chlorophyta: 36 contigs
Most all the Proteobacteria have the same GC ...
written 10 days ago by
kristina.mahan • 100
0
votes
1
answer
646
views
1
answers
... So then you just remove the contigs that are the bacteria from the assembly (green in blobplot)? ...
written 10 days ago by
kristina.mahan • 100
0
votes
0
answers
70
views
0
answers
Comment:
A: Blobtools output files
... and which contigs are contaminants and need to be removed? ...
written 10 days ago by
kristina.mahan • 100
0
votes
0
answers
70
views
0
answers
... ![blobtools graph #1][1]
![blobtools graph #2][2]
Can somebody interpret these blobtools graphs please. My genome is an algal species.
![https://ibb.co/ZmgD7K8][3]
![https://ibb.co/mNf8GBw][4]
[1]: https://ibb.co/mNf8GBw
[2]: https://ibb.co/ZmgD7K8
[3]: https://i.ibb.co/PQWH04h/Screen-S ...
written 10 days ago by
kristina.mahan • 100
0
votes
1
answer
78
views
1
answer
... I have a .gff file someone gave me from an old chloroplast annotation. How can I use that annotation file to annotate my chloroplast genome assembly? ...
written 15 days ago by
kristina.mahan • 100
• updated
14 days ago by
shelkmike • 280
0
votes
0
answers
123
views
0
answers
... Would you expect that contaminant contigs that have not yet been removed- would have gaps in coverage or less coverage? ...
written 15 days ago by
kristina.mahan • 100
0
votes
0
answers
123
views
0
answers
... The illumina sequencing is 2 x 150 bp. The assembly was with pure pac bio reads. I could polished the pac bio assembly using illumina reads with pilon and see if that helps. But I will also try to map illumina reads without trimming or with different trimming parameters. ...
written 24 days ago by
kristina.mahan • 100
0
votes
0
answers
123
views
0
answers
... I trimmed the illumina reads for quality and to trim the adapters. I used Trimmomatic with these parameters:
LEADING:10 TRAILING:10 SLIDINGWINDOW:5:30 MINLEN:150
The genome size is ~ 200 Mb
These are the results from trimming of the illumina reads:
Input Read Pairs: 128614698 Both Surviv ...
written 24 days ago by
kristina.mahan • 100
• updated
15 days ago by
lieven.sterck ♦ 8.7k
0
votes
0
answers
123
views
0
answers
... I assembled a genome using pac bio reads with the Flye Assembler. I then mapped my cleaned up illumina reads using bwa-mem onto the longest contigs and there is gaps in the contigs. Why is this? ...
written 24 days ago by
kristina.mahan • 100
0
votes
0
answers
132
views
0
answers
... yes definitely. It says you can specify contig length but default is 500. I am not specifying contig length and the report says that the stats are based on contigs >= 100,000. So I am not sure what is happening. ...
written 7 weeks ago by
kristina.mahan • 100
Latest awards to kristina.mahan
Popular Question
10 days ago,
created a question with more than 1,000 views.
For Issues with mapping reads onto Reference genome using bwa mem
Supporter
12 weeks ago,
voted at least 25 times.
Popular Question
8 months ago,
created a question with more than 1,000 views.
For Does anybody know how to do a local install of samtools on centos without using sudo?
Popular Question
13 months ago,
created a question with more than 1,000 views.
For Does anybody know how to do a local install of samtools on centos without using sudo?
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 855 users visited in the last hour