User: jean.elbers

gravatar for jean.elbers
jean.elbers1.3k
Reputation:
1,340
Status:
Trusted
Location:
Last seen:
22 hours ago
Joined:
2 years, 9 months ago
Email:
j**********@gmail.com

Posts by jean.elbers

<prev • 199 results • page 1 of 20 • next >
0
votes
1
answer
66
views
1
answers
Comment: C: Where to upload protein coding gene annotation ?
... I wouldn't say I work a lot with annotation- I merely have some experience. I have never used ENA, but I must say that fulfilling annotation requirements set by NCBI may require a few messages back and forth with the curators. As far as I can tell, most people don't submit structural or functional a ...
written 8 days ago by jean.elbers1.3k
0
votes
1
answer
66
views
1
answers
Comment: C: Where to upload protein coding gene annotation ?
... Submitting structural annotations to NCBI is okay, but submitting functional annotations is quite another thing. There is a tool https://genomeannotation.github.io/GAG/ that will help with both, but the functional annotation part is very difficult to go from MAKER annotations to those accepted by NC ...
written 8 days ago by jean.elbers1.3k
0
votes
0
answers
89
views
0
answers
Comment: C: Less and less genes predicted with each iteration of SNAP/MAKER
... No, you were correct that I only showed AED-only filtering steps in the analysis steps, but there were some attempts at combining AED filtering, redundancy removal, and randomization as well that I didn't document but tried. ...
written 8 days ago by jean.elbers1.3k
0
votes
0
answers
89
views
0
answers
Comment: C: Less and less genes predicted with each iteration of SNAP/MAKER
... Well, I had also tried many different things- some similar steps to your pipeline (ex: redundancy removal) and other things (ex:AED filtering, redundancy removal, and randomization), etc. Still to no avail. ...
written 8 days ago by jean.elbers1.3k
0
votes
0
answers
89
views
0
answers
Comment: C: Less and less genes predicted with each iteration of SNAP/MAKER
... @Juke-34 Thank you for the links. You are probably doing a much better job than I have done with training Augustus with MAKER predictions. I have always found the opposite between BUSCO and MAKER training Augustus, but that is at least for mammals and one turtle (Kemp's Ridley sea turtle, marsh rice ...
written 9 days ago by jean.elbers1.3k
0
votes
0
answers
89
views
0
answers
Comment: C: Less and less genes predicted with each iteration of SNAP/MAKER
... Unfortunately, sometimes you can "overtrain" your ab initio gene predictors. More information can be found through searches through the MAKER Developer Google group https://groups.google.com/forum/#!forum/maker-devel. I really don't have much experience with SNAP, rather Augustus. Training Augustus ...
written 9 days ago by jean.elbers1.3k
0
votes
1
answer
364
views
1
answers
Comment: C: Extract flanking region of -500 nt upstream and downstream of BLAST result on ge
... You are welcome! Glad to help! ...
written 10 days ago by jean.elbers1.3k
0
votes
1
answer
364
views
1
answers
Comment: C: Extract flanking region of -500 nt upstream and downstream of BLAST result on ge
... Try it one more time. I forgot to change the `bedtools getfasta` command to force strandness with the `-s` option. ...
written 10 days ago by jean.elbers1.3k
0
votes
1
answer
364
views
1
answers
Comment: C: Extract flanking region of -500 nt upstream and downstream of BLAST result on ge
... Try the following updated code: makeblastdb -in reference.fa -dbtype nucl samtools faidx reference.fa cut -f 1,2 reference.fa.fai > chrom.sizes blastn -db reference -query query.fasta -outfmt 6 -out query.fasta-against-reference.blast cut -f 2,9,10 query.fasta-against-refere ...
written 11 days ago by jean.elbers1.3k
0
votes
1
answer
364
views
1
answers
Comment: C: Extract flanking region of -500 nt upstream and downstream of BLAST result on ge
... This is very strange indeed. I am wondering if it has something to do with a bug in Bedtools (by the way, what version of bedtools are you using?) Just for kicks, can you check the following: samtools faidx reference.fa Sequence1:484754-484980 It should produce >Sequence1:484754-4849 ...
written 11 days ago by jean.elbers1.3k

Latest awards to jean.elbers

Scholar 6 weeks ago, created an answer that has been accepted. For C: bbmap callvariants - how to add sample names, how to get 0/0 alleles back?
Popular Question 6 months ago, created a question with more than 1,000 views. For Minimum coverage for PacBio Arrow
Supporter 7 months ago, voted at least 25 times.
Scholar 8 months ago, created an answer that has been accepted. For C: bbmap callvariants - how to add sample names, how to get 0/0 alleles back?
Commentator 8 months ago, created a comment with at least 3 up-votes. For C: Who are the Greatest Bioinformaticians Of All Time (GBOAT)
Guru 10 months ago, received more than 100 upvotes.
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: What is Read Group platform??
Scholar 11 months ago, created an answer that has been accepted. For C: bbmap callvariants - how to add sample names, how to get 0/0 alleles back?
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: What is Read Group platform??
Appreciated 12 months ago, created a post with more than 5 votes. For C: Racon-Illumina or Pilon?
Scholar 12 months ago, created an answer that has been accepted. For C: bbmap callvariants - how to add sample names, how to get 0/0 alleles back?
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: What is Read Group platform??
Good Answer 12 months ago, created an answer that was upvoted at least 5 times. For C: Racon-Illumina or Pilon?
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: What is Read Group platform??
Commentator 12 months ago, created a comment with at least 3 up-votes. For C: Who are the Greatest Bioinformaticians Of All Time (GBOAT)
Centurion 12 months ago, created 100 posts.
Scholar 13 months ago, created an answer that has been accepted. For C: bbmap callvariants - how to add sample names, how to get 0/0 alleles back?
Appreciated 13 months ago, created a post with more than 5 votes. For C: Racon-Illumina or Pilon?
Scholar 13 months ago, created an answer that has been accepted. For C: bbmap callvariants - how to add sample names, how to get 0/0 alleles back?
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: What is Read Group platform??
Scholar 13 months ago, created an answer that has been accepted. For C: bbmap callvariants - how to add sample names, how to get 0/0 alleles back?
Scholar 17 months ago, created an answer that has been accepted. For C: bbmap callvariants - how to add sample names, how to get 0/0 alleles back?
Scholar 18 months ago, created an answer that has been accepted. For C: bbmap callvariants - how to add sample names, how to get 0/0 alleles back?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 899 users visited in the last hour