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Forum: Bioinformatics 05-16-2018, 01:52 AM
Replies: 0
Views: 202
Posted By morning latte
Has anyone imported IMG blast result to MEGAN?

Hello experts,

I blasted my contigs against the IMG/VR database. When I imported blast output to MEGAN, MEGAN didn't assign any contigs to taxonomy of course. In this case, what can I do? Where...
Forum: Oxford Nanopore 01-16-2017, 10:18 AM
Replies: 32
Views: 16,428
Posted By morning latte
I have one more question to ask. Do you...

I have one more question to ask.

Do you think it would be okay to use Axygen™ AxyPrep Mag™ PCR Clean-up Kits ($142) instead of Agencourt AMPure XP beads ($385)? I am trying to reduce budget for...
Forum: Oxford Nanopore 01-12-2017, 08:13 AM
Replies: 32
Views: 16,428
Posted By morning latte
Hello, What vendor do you use for Tris-HCl...

Hello,

What vendor do you use for Tris-HCl (pH 8.5)? I know Fisher has Tris-HCl with pH 8.0 but can't find any with pH 8.5.
Forum: Oxford Nanopore 01-10-2017, 01:12 PM
Replies: 3
Views: 2,533
Posted By morning latte
Thanks nanos!

Thanks nanos!
Forum: Oxford Nanopore 01-10-2017, 11:20 AM
Replies: 3
Views: 2,533
Posted By morning latte
MinION sequencing kit

Hello experts,

When I am reading some publications using MinION, people used kits named MAP-003 Kits or MAP- 004 Kits for library generation. But when I look at the ONT website, I see three kits,...
Forum: Bioinformatics 12-16-2015, 08:50 AM
Replies: 0
Views: 491
Posted By morning latte
CatchAll to calculate species abundance

Hello,

Has anyone used CatchAll to calculate species richness? I have Illumina reads and contigs and couldn't find a good manual describing what format of data should be used as an input to run...
Forum: Bioinformatics 08-23-2015, 11:36 AM
Replies: 1
Views: 1,589
Posted By morning latte
BLAST out - query coverage

Hello experts,

I have blast output which contains score, e-value, identities, and positives information. I think it is called standard blast. I am wondering if there is any way (by using command)...
Forum: Bioinformatics 08-08-2015, 01:43 PM
Replies: 0
Views: 415
Posted By morning latte
How to create a genome table in QuEST?

Hello experts,

This is my first time to analyze Chip-Seq dataset and I need your advices.

I have run bowtie with my Illumina reads on a remote server. I am trying to create a genome table for...
Forum: Bioinformatics 07-09-2015, 02:20 PM
Replies: 2
Views: 611
Posted By morning latte
Thanks for your answer!

Thanks for your answer!
Forum: Bioinformatics 07-09-2015, 01:48 PM
Replies: 2
Views: 611
Posted By morning latte
Number of paired-end reads

Hello experts,

I have a very simple and stupid question.

Let's say I have five pairs of Illumina reads (10 reads in total). In this case, should I call it ten PE Illumina reads or five PE...
Forum: Bioinformatics 06-18-2015, 08:50 AM
Replies: 1
Views: 1,216
Posted By morning latte
Converting BLAST output to tabular format

Hello experts,

I have run BLASTX without setting any -m option. Now, it would be much better for me to look at tabular format to sort some information out. Should I run BLASTX again with setting m...
Forum: Bioinformatics 02-25-2015, 03:23 PM
Replies: 9
Views: 1,231
Posted By morning latte
Thanks all for the valuable comments. ...

Thanks all for the valuable comments.

Basically, I have tried reformat with multiple sam files and it worked great. I will also try with other comments (e.g. PicardTools). Thanks again!
Forum: Bioinformatics 02-25-2015, 10:34 AM
Replies: 9
Views: 1,231
Posted By morning latte
For input of bowtie2 mapping, i used paired reads...

For input of bowtie2 mapping, i used paired reads with flags -1 and -2.
Forum: Bioinformatics 02-25-2015, 07:40 AM
Replies: 9
Views: 1,231
Posted By morning latte
Thanks! To clarify my goal, I would like to...

Thanks!

To clarify my goal, I would like to obtain fastq files used for mapping from SAM files. Based on comments from Brian Bushnell and diego diaz, it looks doable. Is there any tool for SAM...
Forum: Bioinformatics 02-24-2015, 03:46 PM
Replies: 9
Views: 1,231
Posted By morning latte
SAM file after running bowtie2

Hello experts,

I ran bowtie2 mapping with "local" setting on my illumina datasets a while ago and sam files were generated. Basically, I mapped reads onto assembled contigs. Unfortunately,...
Forum: Bioinformatics 01-30-2015, 06:25 AM
Replies: 7
Views: 2,431
Posted By morning latte
Dear Brian Bushnell, Thanks a lot for the...

Dear Brian Bushnell,

Thanks a lot for the detailed explanation on this. Everything is now very clear.
Forum: Bioinformatics 01-29-2015, 07:22 PM
Replies: 7
Views: 2,431
Posted By morning latte
Dear Brian Bushnell, Thanks a lot for the...

Dear Brian Bushnell,

Thanks a lot for the suggestion. I just ran BBMap on one of my sam files and the summary output looks like below.

Average coverage: 9.75
Percent...
Forum: Bioinformatics 01-29-2015, 06:12 PM
Replies: 7
Views: 2,431
Posted By morning latte
Thanks Sergioo. Unfortunately, I don't have a CLC...

Thanks Sergioo. Unfortunately, I don't have a CLC Genomics Workbench around me. Could you direct me an alternative way if you have any idea? Thanks!
Forum: Bioinformatics 01-29-2015, 05:38 PM
Replies: 7
Views: 2,431
Posted By morning latte
Length of genome covered by reads by mapping

Hello,

I have generated SAM and BAM files after mapping my Illumina reads to a reference genome. Now I want to know how much of the reference genome is covered (aligned/mapped) by reads (e.g. 50%...
Forum: Bioinformatics 01-12-2015, 03:02 PM
Replies: 1
Views: 2,651
Posted By morning latte
blastall error

Hello experts,

I have had no problem running blastall using the command below so far.

blastall -i query.fa -d database -p blastx -e 1e-5 -a 8 -o output.txt

And all of sudden, I am getting...
Forum: Bioinformatics 12-22-2014, 07:03 AM
Replies: 1
Views: 655
Posted By morning latte
Median basepair coverage of reads across contig length

Hello experts,

I am having hard time to understand a method from a metagenomic paper. The author used "median basepair coverage of reads across contig length" to measure base pair coverage of...
Forum: Bioinformatics 12-12-2014, 02:55 PM
Replies: 1
Views: 1,219
Posted By morning latte
Command for vlookup function

Hello experts,

I have large text files that need to be arranged using a function like excel's vlookup. I have been playing with awk command but didn't really come up with a solution. Could anyone...
Forum: Bioinformatics 11-03-2014, 06:17 PM
Replies: 0
Views: 801
Posted By morning latte
qualimap multi

Dear experts,

Has anyone used Qualimap for assessing sequence alignment? I am trying to use "qualimap multi" analysis for multiple bam files. I am running the analysis on a remote server. However,...
Forum: Bioinformatics 10-06-2014, 11:41 AM
Replies: 0
Views: 552
Posted By morning latte
antibiotic resistance gene search

Hello experts,

I am trying to BLAST my Illumina reads (paired-end reads with a length of 100-bp) to antibiotic resistance gene database. I have seen some of papers doing this but all of them used...
Forum: Bioinformatics 10-03-2014, 01:25 PM
Replies: 1
Views: 1,192
Posted By morning latte
Has anyone used GAAS (Genome relative Abundance and Average Size)?

Hello experts,

I have been trying to use GAAS (Genome relative Abundance and Average Size) tool for my metagenomic datasets. I am wondering if anyone has tried out this tool then I could get some...
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