SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 18 of 18
Search took 0.00 seconds.
Search: Posts Made By: kopardev
Forum: Metagenomics 06-03-2016, 11:27 AM
Replies: 1
Views: 2,404
Posted By kopardev
Clustering/Binning Metagenomic contigs with MyCC and 16S sequences

I have tried to use MyCC (http://www.nature.com/articles/srep24175) on samples with varied diversity and I always get very good accuracy between number of clusters and number of 16S sequences found...
Forum: Bioinformatics 06-03-2016, 10:33 AM
Replies: 0
Views: 1,586
Posted By kopardev
Metagenomic contig binning and 16S with MyCC

I have tried to use MyCC (http://www.nature.com/articles/srep24175) on samples with varied diversity and I always get very good accuracy between number of clusters and number of 16S sequences found...
Forum: Metagenomics 06-03-2016, 10:27 AM
Replies: 2
Views: 1,964
Posted By kopardev
Have you tried MyCC...

Have you tried MyCC (http://www.nature.com/articles/srep24175)
Forum: Bioinformatics 01-15-2016, 05:31 AM
Replies: 3
Views: 2,290
Posted By kopardev
Thank you Sven for your questions. These are all...

Thank you Sven for your questions. These are all interesting questions. Our manuscript is available at arxiv for download. I believe this will answer all your questions. I encourage you to download...
Forum: Bioinformatics 01-14-2016, 08:34 AM
Replies: 3
Views: 2,290
Posted By kopardev
FASTQ read filtering/trimming/subsets ... a new approach

Please try MEEPTOOLS and post your comments on how we can improve it.
Thanks.

https://github.com/nisheth/meeptools
Forum: Bioinformatics 07-19-2012, 05:59 AM
Replies: 2
Views: 3,324
Posted By kopardev
1.79769e+308

what does in fold change of 1.79769e+308 mean? Can anyone explain that?
Thanks!
Forum: Bioinformatics 06-29-2012, 08:49 AM
Replies: 2
Views: 2,436
Posted By kopardev
Sff_extract.py script

Sff_extract.py script
Forum: 454 Pyrosequencing 04-09-2012, 10:06 AM
Replies: 1
Views: 1,440
Posted By kopardev
I am having the same problem... Did you find a...

I am having the same problem... Did you find a solution?
Forum: Bioinformatics 04-05-2012, 04:55 AM
Replies: 5
Views: 3,055
Posted By kopardev
Sphil.. do you have a R script for this lying...

Sphil.. do you have a R script for this lying around that you can post here.

I got this after hours of google-ing:


library(lattice)
data<-read.table("contigs.bases.sizes")
y=t(data[2])...
Forum: Bioinformatics 04-04-2012, 12:24 PM
Replies: 5
Views: 3,055
Posted By kopardev
I am looking to visualize an assembly. That is...

I am looking to visualize an assembly. That is make a histogram of contig sizes and possibly color by number of N's. Is there a way to do this quickly??
Forum: Bioinformatics 04-04-2012, 10:57 AM
Replies: 5
Views: 3,055
Posted By kopardev
Contig size distribution vizualizer

Is there something like amos Hawkeye for any assembly fasta file??
Forum: Bioinformatics 03-14-2012, 08:56 AM
Replies: 1
Views: 2,428
Posted By kopardev
Of course, you can do this. Just merge the fna...

Of course, you can do this. Just merge the fna files into a big fna file and create a novoalign index for it. You can always extract the gi numbers from alignment and get back the species/organism...
Forum: Bioinformatics 03-07-2012, 10:31 AM
Replies: 1
Views: 1,997
Posted By kopardev
Post Novoalign miRNA error

I get the following error:

$./novoalign -d ./Homo_sapiens_GRCh37.ndx -f xyz.fastq -F ILM1.8 -m99 -l18 -rAll -c14 -o sam

Interrupted..11
Stack Dump ...
ip = 0x 40060f, sp = 0x ...
Forum: 454 Pyrosequencing 01-06-2012, 12:33 PM
Replies: 7
Views: 4,563
Posted By kopardev
Smile I encountered the same problem recently. The only...

I encountered the same problem recently. The only way around was to trim the 3' adapter from the sff file using biopython and use the new trimmed sff file for assembly. This worked perfectly.
Forum: Bioinformatics 01-03-2012, 12:16 PM
Replies: 7
Views: 12,690
Posted By kopardev
In fact, I have tried using --chunkmbs 1000 and...

In fact, I have tried using --chunkmbs 1000 and still managed to get these errors ... only for paired-end data though.
Forum: Bioinformatics 01-03-2012, 11:59 AM
Replies: 5
Views: 5,364
Posted By kopardev
Post Aligning paired end Illumina data with Bowtie

I have 2 fastq files read1.fastq and read2.fastq.
If I align read1.fastq to the reference genome, I get a set of readids that align. Lets say a1, a2, a3, a4, a5, a6, a7, a8, a9 for simplicity.
If I...
Forum: Bioinformatics 01-03-2012, 11:49 AM
Replies: 1
Views: 2,021
Posted By kopardev
Post Discrepancy in paired-end Illumina data

I have a variety of paired end data sets from Illumina and these are some of their sequence lengths:
Read1 Read2
103 110
103 107
101 101
98 ...
Forum: Bioinformatics 01-03-2012, 11:42 AM
Replies: 7
Views: 12,690
Posted By kopardev
I get similar warnings when I use paired end...

I get similar warnings when I use paired end data. But if I align read1 and read2 separately, I do not get any warnings. Solutions/pointers are appreciated.
Thanks,
Vishal
Showing results 1 to 18 of 18

 


All times are GMT -8. The time now is 05:37 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO