User: Moses

gravatar for Moses
Moses60
Reputation:
60
Status:
Trusted
Location:
united states/ Bloomingtion/ Indiana University Bloomington
Last seen:
1 month ago
Joined:
4 years, 10 months ago
Email:
m****************@gmail.com

Posts by Moses

<prev • 52 results • page 1 of 6 • next >
0
votes
1
answer
100
views
1
answers
Comment: C: taxonomic identification least common ancestor approach
... oh I see, right now I'm running the lineage_wf command over my bins, maybe I should also try and run tree_qa after it's done. Thanks for the advice. ...
written 4 weeks ago by Moses60
0
votes
1
answer
100
views
1
answers
Comment: C: taxonomic identification least common ancestor approach
... taxonomy_wf sounds more like identifying a particular phylum, and involves pre-specifying the phylum beforehand, The bins that I want to do taxonomic identification are very diverse and I don't see how I can run the taxonomy_wf command, instead lineage_wf is just extracting general marker genes I ...
written 4 weeks ago by Moses60
0
votes
1
answer
100
views
1
answers
Comment: C: taxonomic identification least common ancestor approach
... Hi, thank you for your comments and sorry for the late reply. I actually was looking into checkm and trying to get it running. It uses Python2 unfortunately and I had to roll back my python version to 2 and install dependencies etc. I just issued a run and see what it results. Thank you for your sug ...
written 4 weeks ago by Moses60
0
votes
1
answer
100
views
1
answer
taxonomic identification least common ancestor approach
... Hi all, I have 3,300 binned contigs (bacterial sequences) that I would like to know the species (where possible) or the least common ancestor explaining what clades each of these bins would be coming from. I understand that MEGAN is designed to do that, however I have my build my own phylogenetic t ...
phylogeny taxonomy genus phylum written 5 weeks ago by Moses60 • updated 5 weeks ago by Asaf5.6k
0
votes
2
answers
216
views
2
answers
Comment: C: do paired end reads both mapped to the same gene appear consecutive to each othe
... thanks Rob for this guide. I made a postprocessing script where I check if there are reads like that and if both of the pairs are maped to the same gene/genome then I rearrange them such that read1 to gene and read2 to the same gene appear immidiately consecutive in the sam file. Also in the script ...
written 9 weeks ago by Moses60
0
votes
2
answers
216
views
2
answers
Comment: C: do paired end reads both mapped to the same gene appear consecutive to each othe
... yeah I'm working on my own script to take care of this. But what's surprising me is that in most of the cases (multimapped cases) Bowtie2 is respecting the order of pairing in the sam file. i.e. Let's say I have a paired end read R1 and R2, that is mapped to 3 different genes g1,g2 and g3. In most o ...
written 10 weeks ago by Moses60
0
votes
2
answers
216
views
2
answers
Comment: C: do paired end reads both mapped to the same gene appear consecutive to each othe
... I got the same result unfortunately :(( I updated my original post and included a snapshot of the reasd as they appear in my fastq files, maybe that would help a bit more. The command I used with bowtie2 now is the following: bowtie2 --reorder -a -x ../target_gene_indices/S1/S1_target_seqs_db - ...
written 10 weeks ago by Moses60
1
vote
2
answers
216
views
5 follow
2
answers
do paired end reads both mapped to the same gene appear consecutive to each other in SAM file (using bowtie2)
... Hi all, I'm using bowtie2 to map short illumina reads (101 base long reads) back to genes as my reference database. However I noticed something odd in the sam file earlier. I'm using paired end reads and keeping multimaps also. I originally thought when there is a paired end read that maps to the ...
bowtie2 sam shortreads written 10 weeks ago by Moses60 • updated 10 weeks ago by Devon Ryan90k
0
votes
0
answers
182
views
0
answers
Comment: C: combining phylogenetic trees into a consensus super Tree
... Thank you for this. I am looking into clann documentation now. Is it necessary for the program to know which leaf nodes match with each other aprioiri? In my case I just have many gene trees and I do not know which leaves are coming from which species in any of them, I just want to somehow do an opt ...
written 3 months ago by Moses60
0
votes
0
answers
182
views
0
answers
combining phylogenetic trees into a consensus super Tree
... Hi all, I have around 50 unrotoed phylogenetic trees that are generated using FastTree from 51 different gene families coming from different number of species. Not all of my trees have the same number of leaf nodes. Some might have a few more some a few less. I want to combine these trees into o ...
phylogenetics tree written 3 months ago by Moses60

Latest awards to Moses

Popular Question 8 weeks ago, created a question with more than 1,000 views. For running CD-hit from python scripts
Popular Question 8 weeks ago, created a question with more than 1,000 views. For retrieving all Human Mouse between species out-paralogs
Great Question 3.0 years ago, created a question with more than 5,000 views. For running modeller through python scripts
Popular Question 3.0 years ago, created a question with more than 1,000 views. For running CD-hit from python scripts
Popular Question 3.0 years ago, created a question with more than 1,000 views. For FASTA and PIR formats in python
Popular Question 3.0 years ago, created a question with more than 1,000 views. For get the uniprot accession from ensembl protein ID
Popular Question 3.0 years ago, created a question with more than 1,000 views. For difference between imports in biojava
Popular Question 3.7 years ago, created a question with more than 1,000 views. For running modeller through python scripts

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1781 users visited in the last hour