User: pdm37

gravatar for pdm37
pdm3710
Reputation:
10
Status:
New User
Location:
United States
Last seen:
2 months, 2 weeks ago
Joined:
3 years, 7 months ago
Email:
p****@cornell.edu

Posts by pdm37

<prev • 9 results • page 1 of 1 • next >
0
votes
0
answers
207
views
0
answers
Comment: C: finding variants in the low to no coverage areas of bacterial genomes
... Thanks for the suggestions re: SPADES, prokka etc. I'll give it a go! ...
written 10 weeks ago by pdm3710
0
votes
0
answers
207
views
0
answers
Comment: C: finding variants in the low to no coverage areas of bacterial genomes
... I've tried looking for indels specifically. I used pindel, which supposedly finds indels, as well as bbmap which was recommended to me here on biostars. I was able to identify an known insertion in another genome that I was working with, but nothing else popped up. ...
written 10 weeks ago by pdm3710
0
votes
0
answers
207
views
0
answers
Comment: C: finding variants in the low to no coverage areas of bacterial genomes
... less than 1% of reads are going unmapped. I was thinking of just sequencing a few of the regions with Sanger ...
written 10 weeks ago by pdm3710
3
votes
0
answers
207
views
0
answers
finding variants in the low to no coverage areas of bacterial genomes
... Hello all, I have two closely related bacterial strains (mutants of the same wildtype strain for which I have a fully sequenced, closed and annotated genome) that exhibit an interesting phenotype. We have sequenced the genomes of the two strains of interest with MiSeq. I have been able to identify ...
alignment snp written 11 weeks ago by pdm3710
0
votes
1
answer
252
views
1
answers
Comment: C: pindel not picking up on a lab-made gene knockout deletion
... thank you for the suggestion! The alignment has a gap in that region, or rather all the bp in the reads that span it are crossed out (due to mismatch, which is due to the insertion, I would presume). I used BWA mem as the aligner. ...
written 3 months ago by pdm3710
0
votes
1
answer
252
views
1
answers
Comment: C: pindel not picking up on a lab-made gene knockout deletion
... the deletion is 199 bp, the inserted sequence is 251bp. I can see the deletion in the bam file and the insertion comes up in the unmapped reads ...
written 3 months ago by pdm3710
3
votes
1
answer
252
views
1
answer
pindel not picking up on a lab-made gene knockout deletion
... I have used pindel (version 0.2.4t) to look for indels in two strains that had a gene knocked out and replaced with an antibiotic resistance gene. The two mutants grew despite the knockout and we were looking for other mutations that may have led to this phenotype. Pindel didn't identify the knockou ...
pindel written 3 months ago by pdm3710 • updated 3 months ago by Brian Bushnell15k
2
votes
1
answer
1.3k
views
1
answer
How to identify transposons in a non-model organism transcriptome
... I have several assembled, annotated transcriptomes of non-model organisms (fish). I would like to identify what transposons are present in these transcriptomes (LTR, SINEs, LINEs etc) and compare them. I am currently trying to use RepeatMasker to identify them using a clade specific library from Rep ...
next-gen rna-seq blast written 3.6 years ago by pdm3710 • updated 2.1 years ago by Biostar ♦♦ 20
0
votes
1
answer
1.5k
views
1
answer
RepeatMasker errors and missing output files
... I am using RepeatMasker to identify retrotransposons in my non-model organism's assembled transcriptome. When I tried the following: RepeatMasker xxx.fa -species vertebrates -engine RMBlast it produced a .masked file and a .cat file but no .tbl and lots and lots of .err files (trfResultsxxxx.err) ...
software error written 3.6 years ago by pdm3710 • updated 3.6 years ago by Buttonwood30

Latest awards to pdm37

Popular Question 3.5 years ago, created a question with more than 1,000 views. For How to identify transposons in a non-model organism transcriptome
Popular Question 3.5 years ago, created a question with more than 1,000 views. For RepeatMasker errors and missing output files

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1586 users visited in the last hour