User: skbrimer

gravatar for skbrimer
skbrimer350
Reputation:
350
Status:
Trusted
Location:
United States
Last seen:
4 days, 11 hours ago
Joined:
2 years, 7 months ago
Email:
s*******@gmail.com

Posts by skbrimer

<prev • 146 results • page 1 of 15 • next >
1
vote
0
answers
111
views
0
answers
MLST ST Interpretations
... Hello Hive mind, I know it's the weekend and all but I'm going to try anyway. Earlier I posted about sequencing several strep suis genomes and had issues with alignment. I got some good advice to use Mauve which helped a lot still not done with it and I need to go and update that post as well. Any ...
ngs mlst written 28 days ago by skbrimer350
0
votes
0
answers
148
views
0
answers
Comment: C: Streptococcus genome alignments
... Thank you for the link! ...
written 4 weeks ago by skbrimer350
0
votes
0
answers
148
views
0
answers
Comment: C: Streptococcus genome alignments
... Also, and I suspect unsurprisingly (yey circular genomes), it looks like the start of the genome and the end of the genome is in one contig of the de novo build. ...
written 4 weeks ago by skbrimer350
0
votes
0
answers
148
views
0
answers
Comment: C: Streptococcus genome alignments
... The Mauve alignment shows lots of gene shuffling, this was a great idea! Is it possible to use this alignment to order the contigs? ...
written 4 weeks ago by skbrimer350
0
votes
0
answers
148
views
0
answers
Comment: C: Streptococcus genome alignments
... Sorry, I am using BWA as the mapper and SPAdes as the de novo assembler. TMAP is a variant of BWA and I do use both. I have found that they give only slightly different builds since the read quality of Ion Torrent has improved. For most builds I do use BWA over TMAP mostly due to the speed. There ar ...
written 4 weeks ago by skbrimer350
0
votes
0
answers
148
views
0
answers
Comment: C: Streptococcus genome alignments
... I will download and give it a try ...
written 4 weeks ago by skbrimer350
0
votes
0
answers
148
views
0
answers
Comment: C: Streptococcus genome alignments
... HAHA! The power is back on! According to samtools flagstats 82% of the contigs map back to the assembly, however they get clipped heavily and the output in IGV matched closely to the short read mapping. ![top, short reads. bottom contigs][1] [1]: https://ibb.co/h4eWL5 ...
written 4 weeks ago by skbrimer350
0
votes
0
answers
148
views
0
answers
Comment: C: Streptococcus genome alignments
... Oh. Excellent question I didn't look at that. What I meant by basically the same is when I look at the mapping in igv I get the same areas of coverage. I will look at the total mapping and get back to you. We currently don't have power due to a storm but when it comes back I will look. ...
written 5 weeks ago by skbrimer350
0
votes
0
answers
148
views
0
answers
Comment: C: Streptococcus genome alignments
... Also because of the library I know that the de novo mapping should leave gaps due to the repeat areas but I am getting large drop outs. It's more like I have a really bad reference. However I have been reading other strep suis papers and they all seem to map to this ref. ...
written 5 weeks ago by skbrimer350
0
votes
0
answers
148
views
0
answers
Comment: C: Streptococcus genome alignments
... Pretty much the same thing that I get when I just map the reads. If I use bwa mem I get a lot of hard clipping. I need to play with the stringency I think. I was also going to try either the pacbio or nanopore settings. ...
written 5 weeks ago by skbrimer350

Latest awards to skbrimer

Popular Question 5 weeks ago, created a question with more than 1,000 views. For Can Q10 be better than Q30
Scholar 10 weeks ago, created an answer that has been accepted. For A: Submitting several BLAST queries using NCBIWWW at once
Popular Question 6 months ago, created a question with more than 1,000 views. For Can Q10 be better than Q30
Centurion 13 months ago, created 100 posts.
Scholar 15 months ago, created an answer that has been accepted. For A: Submitting several BLAST queries using NCBIWWW at once
Scholar 16 months ago, created an answer that has been accepted. For A: Submitting several BLAST queries using NCBIWWW at once
Scholar 16 months ago, created an answer that has been accepted. For A: Submitting several BLAST queries using NCBIWWW at once
Scholar 16 months ago, created an answer that has been accepted. For A: Submitting several BLAST queries using NCBIWWW at once
Scholar 18 months ago, created an answer that has been accepted. For A: Submitting several BLAST queries using NCBIWWW at once
Scholar 18 months ago, created an answer that has been accepted. For A: Submitting several BLAST queries using NCBIWWW at once
Scholar 18 months ago, created an answer that has been accepted. For A: Submitting several BLAST queries using NCBIWWW at once
Supporter 20 months ago, voted at least 25 times.
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: Thrown Into A Bioinformatics Position
Scholar 2.1 years ago, created an answer that has been accepted. For A: Submitting several BLAST queries using NCBIWWW at once
Scholar 2.2 years ago, created an answer that has been accepted. For A: Submitting several BLAST queries using NCBIWWW at once
Scholar 2.2 years ago, created an answer that has been accepted. For A: Submitting several BLAST queries using NCBIWWW at once
Scholar 2.3 years ago, created an answer that has been accepted. For A: Submitting several BLAST queries using NCBIWWW at once
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Using Biopython and BLAST+ to automate de novo viral contig sorting

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 866 users visited in the last hour