Forum: Bioinformatics
02-13-2017, 06:57 PM
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Replies: 2
Views: 2,352
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...
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Forum: Bioinformatics
01-19-2017, 12:27 PM
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Replies: 7
Views: 2,994
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Forum: Bioinformatics
01-19-2017, 10:25 AM
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Replies: 7
Views: 2,994
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Forum: Bioinformatics
01-18-2017, 02:10 PM
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Replies: 7
Views: 2,994
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Forum: Bioinformatics
01-18-2017, 11:11 AM
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Replies: 7
Views: 2,994
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...
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Forum: Bioinformatics
12-20-2016, 09:37 AM
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Replies: 9
Views: 4,231
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Forum: Bioinformatics
12-17-2016, 12:26 PM
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Replies: 9
Views: 4,231
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?...
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Forum: Bioinformatics
12-12-2016, 07:48 PM
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Replies: 3
Views: 5,052
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...
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Forum: Bioinformatics
12-12-2016, 05:52 PM
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Replies: 3
Views: 5,052
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!
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Forum: Bioinformatics
11-29-2016, 01:39 PM
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Replies: 1
Views: 4,534
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...
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Forum: Bioinformatics
11-27-2016, 07:13 PM
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Replies: 10
Views: 4,562
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Forum: Bioinformatics
11-27-2016, 07:03 PM
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Replies: 10
Views: 4,562
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Forum: Bioinformatics
11-25-2016, 02:32 PM
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Replies: 10
Views: 4,562
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Forum: Bioinformatics
11-25-2016, 11:05 AM
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Replies: 10
Views: 4,562
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...
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Forum: Bioinformatics
11-25-2016, 12:01 AM
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Replies: 3
Views: 4,500
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...
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Forum: Bioinformatics
11-24-2016, 09:10 PM
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Replies: 3
Views: 4,500
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...
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Forum: Bioinformatics
11-24-2016, 08:23 PM
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Replies: 6
Views: 3,309
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...
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Forum: Bioinformatics
11-24-2016, 03:12 PM
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Replies: 6
Views: 3,309
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Forum: Bioinformatics
11-24-2016, 02:45 PM
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Replies: 6
Views: 3,309
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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