User: bitpir

gravatar for bitpir
bitpir70
Reputation:
70
Status:
Trusted
Location:
Last seen:
13 hours ago
Joined:
2 years, 1 month ago
Email:
r*******@gmail.com

Posts by bitpir

<prev • 39 results • page 1 of 4 • next >
0
votes
1
answer
143
views
1
answers
Comment: C: getting a combination of all predicted genes
... Thanks for the response! I actually made a mistake in the desired result, it's corrected now. I aim to get all of the orfs predicted by mga and genemark. However, when the same orf is predicted in the same region, I'll give preference to the longer one: NC_003552.1 mga cds 1 1500 133.183 - ...
written 28 days ago by bitpir70
0
votes
1
answer
143
views
5 follow
1
answer
getting a combination of all predicted genes
... Hello, I was wondering if anyone knows the best way to doing this. I have results from 2 ORF predictors, Mga and Genemark. I now want to combine all the predicted ORFs together. I would like to keep all overlapping ORFs and also the genes that are slightly longer (e.g. +10bp). The MGA result is as ...
bedtools gff written 28 days ago by bitpir70 • updated 28 days ago by Alex Reynolds24k
0
votes
1
answer
140
views
1
answers
Comment: C: getting feature annotations for all NCBI Refseq sequences
... Ah! Just found the [answer][1] to my question, for the second part at least :) [1]: https://www.biostars.org/p/221188/ ...
written 4 weeks ago by bitpir70
0
votes
1
answer
140
views
1
answers
Comment: C: getting feature annotations for all NCBI Refseq sequences
... great, thank you! My virus db includes [View all RefSeq and Neighbor nucleotide records][1], will all of the viruses be captured in the summary file? I was thinking of finding all the NC_ accession number to a particular assembly accession number [(e.g. NC_011750.1 --> GCF_000026345.1)][2]. I ha ...
written 4 weeks ago by bitpir70
0
votes
1
answer
140
views
1
answers
Comment: C: getting feature annotations for all NCBI Refseq sequences
... Awesome! Thank you so much for your answer, this is super helpful! Are the sequences from the Refseq/release represented in the assembly_summary_refseq.txt? And in case of viruses [e.g. https://www.ncbi.nlm.nih.gov/nuccore/LC340031.1][1], is there a similar assembly_summary file where I can get all ...
written 4 weeks ago by bitpir70
2
votes
1
answer
140
views
1
answer
getting feature annotations for all NCBI Refseq sequences
... Hi, I was wondering if there's a way to download all feature annotations (Gene; CDS; rRNA; tRNA; ncRNA; repeat_region) of all the Refseq sequences (ftp://ftp.ncbi.nih.gov/refseq/release/) from NCBI? I can't seem to find it anywhere on the web or NCBI. Something like GFF for Genbank sequences would b ...
ncbi annotation refseq cds written 5 weeks ago by bitpir70 • updated 5 weeks ago by genomax49k
0
votes
1
answer
127
views
1
answers
Comment: C: IGV tracks gene annotation
... I see! Got it, thank you so much for pointing out. That's really weird that Glimmer GFF has that kind of format. I'll check again with the formatting with that file. Thanks! ...
written 5 weeks ago by bitpir70
0
votes
1
answer
127
views
1
answers
Comment: C: IGV tracks gene annotation
... Hmm, I don't think that's the problem because there are other orfs that go in reverse direction too (HSP_RS15385). I found this answer from another site (https://biology.stackexchange.com/questions/68431/clarification-on-refseq-genes-track-on-igv) The thinner line is supposed to be untranslated regi ...
written 6 weeks ago by bitpir70
2
votes
1
answer
127
views
1
answer
IGV tracks gene annotation
... Hi there, I'm trying to visualize a reference genome in IGV and annotate the genes using a custom made GFF file. The snapshot of the IGV looks something like this. I am particularly curious about the pink labeled track. The GFF for the pink track looks something like this: NC_023010.2 glimmer c ...
gene gff igv written 6 weeks ago by bitpir70 • updated 6 weeks ago by h.mon15k
0
votes
0
answers
97
views
0
answers
complete and partial ORF identification
... Hi there, Does anyone know if Glimmer and Genemark can predict both complete and partial genes? (I know MGA does). Is there a way to see which is which in the output file? Thanks! ...
orf glimmer genemark gene prediciton written 8 weeks ago by bitpir70

Latest awards to bitpir

Popular Question 6 days ago, created a question with more than 1,000 views. For fold enrichment calculation for exome sequencing
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: how to plot multi pheatmap into one figure
Scholar 10 months ago, created an answer that has been accepted. For A: do blast search using gi numbers
Popular Question 16 months ago, created a question with more than 1,000 views. For samtools counting unique mapped reads

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1593 users visited in the last hour