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Forum: Bioinformatics 02-13-2017, 05:57 PM
Replies: 2
Views: 2,371
Posted By hamcan
PCoA Plots

Hi Everyone,
I have HiSequencing data that I want to set up PCoA plots for.
These are environmental samples and I want to look at the diversity between the samples in terms of taxonomy.
What...
Forum: Bioinformatics 01-19-2017, 11:27 AM
Replies: 7
Views: 3,026
Posted By hamcan
that makes perfect sense!!! Thank you so much

that makes perfect sense!!! Thank you so much
Forum: Bioinformatics 01-19-2017, 09:25 AM
Replies: 7
Views: 3,026
Posted By hamcan
First step I'm doing is using Trimmomatic to trim...

First step I'm doing is using Trimmomatic to trim and remove my adapters using the PE setting:

java -jar trimmomatic-0.36.jar PE File1_L001_R1_001.fastq File1_L001_R2_001.fastq...
Forum: Bioinformatics 01-18-2017, 01:10 PM
Replies: 7
Views: 3,026
Posted By hamcan
i know i should expect a decrease but i'm getting...

i know i should expect a decrease but i'm getting an increase. do you know why?
Forum: Bioinformatics 01-18-2017, 10:11 AM
Replies: 7
Views: 3,026
Posted By hamcan
Number of Reads Increasing

Hi there,
I trimmed my reads and then merged them using FLASh. However, I found that the number of reads before processing (trim and merge) is lower than the number of reads after processing.
Is...
Forum: Bioinformatics 12-20-2016, 08:37 AM
Replies: 9
Views: 4,268
Posted By hamcan
thanks everyone! how about to find the number...

thanks everyone!
how about to find the number of bases?
Forum: Bioinformatics 12-17-2016, 11:26 AM
Replies: 9
Views: 4,268
Posted By hamcan
Number of Reads

Hi there,
I have Illumina HiSeq fastq output files. I want to know how I can find out the number of reads per sample before and after processing using unix.
Any commands that you might know of?...
Forum: Bioinformatics 12-12-2016, 06:48 PM
Replies: 3
Views: 5,162
Posted By hamcan
Thanks for responding so quickly! Well I ran a...

Thanks for responding so quickly!
Well I ran a HiSeq run on environmental water samples. So it's a metagenomics experiment. The purpose of the experiment is to look at what species are predominant...
Forum: Bioinformatics 12-12-2016, 04:52 PM
Replies: 3
Views: 5,162
Posted By hamcan
Average Insert Size

Hi there,
I ran an Illumina HiSeq run 2x250 and wanted to know how I could find out the average insert size from my fastq files?

Thanks in advance!
Forum: Bioinformatics 11-29-2016, 12:39 PM
Replies: 1
Views: 4,614
Posted By hamcan
Trimmomatic IlluminaClip

Hi everyone,

I ran a 2x250bp HiSeq run on water samples to analyze what species of bacteria are present. So the whole aim of my project is to look at the species abundance and the functional...
Forum: Bioinformatics 11-27-2016, 06:13 PM
Replies: 10
Views: 4,591
Posted By hamcan
This would explain the 5' end, but how about the...

This would explain the 5' end, but how about the 3' end?
Forum: Bioinformatics 11-27-2016, 06:03 PM
Replies: 10
Views: 4,591
Posted By hamcan
Hey, it was adapter trimmed at the 3' end! So i'm...

Hey, it was adapter trimmed at the 3' end! So i'm not sure what is going on..suggestions?
Forum: Bioinformatics 11-25-2016, 01:32 PM
Replies: 10
Views: 4,591
Posted By hamcan
Below are the pictures of the FastQC failed...

Below are the pictures of the FastQC failed reports:
Forum: Bioinformatics 11-25-2016, 10:05 AM
Replies: 10
Views: 4,591
Posted By hamcan
FastQC Report

I ran a HiSeq on environmental samples and the purpose of the run was to blast my sequences against the NCBI-nr database to see what species my reads match to. I am not doing a denovo assembly or...
Forum: Bioinformatics 11-24-2016, 11:01 PM
Replies: 3
Views: 4,556
Posted By hamcan
Thank you so much for your response! After I...

Thank you so much for your response! After I merge should I concatenate the unpaired files to the merged files? I'm running a BLAST to referenced bacterial genomes.
Another question, for removal of...
Forum: Bioinformatics 11-24-2016, 08:10 PM
Replies: 3
Views: 4,556
Posted By hamcan
Adaptor Removal with Trimmomatic

Hi there,

I ran a HiSeq2500 run and found that I had adaptor sequences still present.
I first used Trimmomatic to simulatenously remove the adaptor sequences and trim the sequences to a good...
Forum: Bioinformatics 11-24-2016, 07:23 PM
Replies: 6
Views: 3,354
Posted By hamcan
Okay thanks!! I am planning on doing cutadapt...

Okay thanks!!
I am planning on doing cutadapt to remove the adaptor sequences. Then I will merge my sequences and then Trim them using trimmomatic so that I can blast them against the NCBI-nr...
Forum: Bioinformatics 11-24-2016, 02:12 PM
Replies: 6
Views: 3,354
Posted By hamcan
So should I first use trimmomatic then to remove...

So should I first use trimmomatic then to remove the adaptors and to overall trim the sequences at once? Then merge?

Thank you!
Forum: Bioinformatics 11-24-2016, 01:45 PM
Replies: 6
Views: 3,354
Posted By hamcan
Illumina HiSeq2500 Pipeline Question

Hi there,
I have just received my Illumina HiSeq data back. I have 2x250bp runs (so forward and reverse reads).

I ran a FASTQC and found that I have an adaptor sequence present in my data. Should...
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