User: DC7

gravatar for DC7
DC720
Reputation:
20
Status:
New User
Location:
India
Last seen:
6 hours ago
Joined:
3 months, 3 weeks ago
Email:
d**********@phd.nitdgp.ac.in

Posts by DC7

<prev • 63 results • page 1 of 7 • next >
0
votes
1
answer
44
views
1
answer
Relative abundance heatmap interpretation
... HI community!!! I have a very basic question regarding heatmap. I have never done heatmap analysis before. I have generated a relative abundance heatmap from test and control samples. Can you please tell how much colour difference should I consider to conclude that there is an increase or decrease ...
microbiome heatmap written 1 day ago by DC720 • updated 1 day ago by antonioggsousa380
1
vote
0
answers
116
views
0
answers
bash script for catenating many paired end files
... Hi friends!!! I have around 300 paired-end files from 150 samples (1 forward and 1 reverse read for each sample). I want to catenate respective forward and reverse reads for each of the samples. The samples are named like: **SRR2155174_1.fastq SRR2155174_2.fastq SRR2155319_1.fastq SRR2155319_2.f ...
catenation written 4 days ago by DC720
1
vote
1
answer
68
views
1
answer
stacked barplot color choice
... Hi community!!! I am generating stacked barplots from mothur output data by phyloseq package. I have got around 60 genus (abundance >1%). I don't know how can I color all of them, because it requires 60 colors. And, it's very hard to differentiate between the colors in naked eye. Any suggestion ...
R metagenomics 16s phyloseq written 7 days ago by DC720 • updated 7 days ago by antonioggsousa380
0
votes
0
answers
54
views
0
answers
Visualise metaphlan output with KRONA
... Hi biostars!!! Is there anyone using krona with metaphlan taxonomic profile output file? I am struggling with krona. The interactive pie chart is not giving the same abundance to that of the profile file. My command: $python3 metaphlan2krona.py --profile baseline_profile.txt --krona baseline_pr ...
wgs metaphlan metagenome krona written 11 days ago by DC720
0
votes
0
answers
79
views
0
answers
Comment: C: Cut off for "dist.seqs" and "cluster" step in MOTHUR for "genus" level analysis
... Sir, can I do phylotype analysis at different taxa levels? Because, if I do OTU analysis at different cutoffs, I am getting a single genus multiple times in the heatmap. Also, after phylotype analysis I am getting 34 classified genus. Do you think 34 is a very low number of genus? May there be any ...
written 13 days ago by DC720
0
votes
0
answers
79
views
0
answers
Comment: C: Cut off for "dist.seqs" and "cluster" step in MOTHUR for "genus" level analysis
... Sir, I'm confused. Because, in `Phyloseq` the `import_mothur` functions import the `taxonomy` file, `shared` file and `tree file`. For generating these three files shouldn't execute these steps? Thanks, DC7 ...
written 13 days ago by DC720
1
vote
0
answers
79
views
0
answers
Cut off for "dist.seqs" and "cluster" step in MOTHUR for "genus" level analysis
... Hi community!!! I want to compare the control and test samples at “**Genus**” level. Can anyone please tell me what cut off should I use at `dist.seqs` and `cluster` step? Thanks and Regards, DC7 ...
mothur metagenome 16s written 13 days ago by DC720
0
votes
0
answers
66
views
0
answers
Number of OTUs obtained from mothur analysis
... Hi friends!!! I have analysed gut metagenome 16S rRNA data with MOTHUR package. I am getting aroung 23,000 OTUs (cut off= 0.03) in my output file. Is such high number of OTUs abnormal? Thanks and regards, DC7 ...
otu mothur 16s written 13 days ago by DC720
0
votes
1
answer
76
views
1
answers
Comment: C: mothur output visualisation with Phyloseq: unable to order the x-axis
... ok sir. Thanks. Now I understand ...
written 15 days ago by DC720
0
votes
1
answer
76
views
1
answers
Comment: C: mothur output visualisation with Phyloseq: unable to order the x-axis
... so, should the label and breaks be same? ...
written 15 days ago by DC720

Latest awards to DC7

Rising Star 16 days ago, created 50 posts within first three months of joining.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1102 users visited in the last hour