User: DC7
DC7 • 20
- 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
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... 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 ...
written 1 day ago by
DC7 • 20
• updated
1 day ago by
antonioggsousa • 380
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... 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 ...
written 4 days ago by
DC7 • 20
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... 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 ...
written 7 days ago by
DC7 • 20
• updated
7 days ago by
antonioggsousa • 380
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... 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 ...
written 11 days ago by
DC7 • 20
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... 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
DC7 • 20
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... 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
DC7 • 20
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... 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 ...
written 13 days ago by
DC7 • 20
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... 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 ...
written 13 days ago by
DC7 • 20
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... ok sir. Thanks. Now I understand ...
written 15 days ago by
DC7 • 20
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... so, should the label and breaks be same? ...
written 15 days ago by
DC7 • 20
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created 50 posts within first three months of joining.
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