Forum: Metagenomics
02-12-2021, 04:19 PM
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Replies: 0
Views: 225
16S library preparation - multiple bands
Hi,
I am carrying out test PCRs for 16S amplicon sequencing on Illumina MiSeq. I am using standard V4 primers: 515F/806R. The aim is to profile the microbiome of fish guts under different...
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Forum: Bioinformatics
11-12-2020, 04:58 PM
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Replies: 138
Views: 50,874
Strange peak at beginning of M-bias plots
Hi,
I have generated RRBS read data, which I have filtered and trimmed using Trim Galore and then aligned to a reference genome using Bismark. Three independent sequencing libraries were created...
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Forum: Epigenetics
03-19-2019, 10:18 PM
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Replies: 0
Views: 3,500
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Forum: Bioinformatics
03-05-2019, 10:49 PM
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Replies: 0
Views: 1,387
SNP calling from RRBS data
Hello,
I am interested in calling SNPs from reduced-representation bisulfite sequencing (RRBS) read data. The purpose of this analysis is to generate a FST value among study groups to quantify...
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Forum: Bioinformatics
03-05-2019, 01:18 PM
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Replies: 0
Views: 1,497
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Forum: Bioinformatics
12-07-2017, 08:36 AM
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Replies: 0
Views: 1,258
BiSeq - How to handle covariates?
Hi,
I am attempting to use BiSeq (Hebestreit et al. 2013) to delineate DMRs among treatment groups in Bismark aligned RRBS data
I have made a successful preliminary run through of the BiSeq...
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Forum: Bioinformatics
10-24-2017, 11:39 AM
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Replies: 648
Views: 192,685
Hi Felix,
I managed to get the script to...
Hi Felix,
I managed to get the script to work by having all the files (input, output) in the same directory as the bismark2Bedgraph script.
I could not find anything wrong with the file...
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Forum: Bioinformatics
10-20-2017, 07:54 AM
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Replies: 648
Views: 192,685
Hi,
I am having trouble getting the...
Hi,
I am having trouble getting the bismark2bedGraph software in the Bismark package to run. I have successfully aligned my RRBS reads to my reference genome and then used...
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Forum: Bioinformatics
04-25-2017, 02:46 AM
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Replies: 648
Views: 192,685
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Forum: Bioinformatics
04-24-2017, 07:39 AM
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Replies: 648
Views: 192,685
Hi,
I have been using Bismark to align RRBS...
Hi,
I have been using Bismark to align RRBS read data to a reference genome. Up until now I have been using the default alignment settings with Bowtie2. However I want to find out if these are...
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Forum: Bioinformatics
04-17-2017, 02:17 PM
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Replies: 138
Views: 50,874
Choosing minimum RRBS read length in Trim Galore!
I am new to the bioinformatic analysis of RRBS data. I am using Trim Galore! to QC and adapter trim my RRBS read data. I have generated single-end 75bp reads on an Illumina NextSeq.
The default...
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Forum: Sample Prep / Library Generation
07-08-2016, 03:27 AM
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Replies: 6
Views: 8,511
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Forum: Sample Prep / Library Generation
06-20-2016, 01:43 AM
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Replies: 6
Views: 8,511
Thanks for the reply,
It seems like you have...
Thanks for the reply,
It seems like you have a lot of experience carrying out DNA extractions from RNAlater, have you had a chance to compare the extractions for yield/quality to those of the same...
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Forum: Sample Prep / Library Generation
06-14-2016, 06:27 AM
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Replies: 6
Views: 8,511
Apologies for the lack of detail.
I am using...
Apologies for the lack of detail.
I am using fish liver tissue.
It is a tissue that I have never had too much problem carrying out extractions with before (for ethanol stored tissue). In fact...
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Forum: Sample Prep / Library Generation
06-14-2016, 03:49 AM
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Replies: 6
Views: 8,511
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Forum: Bioinformatics
07-16-2015, 08:14 AM
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Replies: 0
Views: 769
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Forum: RNA Sequencing
10-16-2012, 05:52 AM
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Replies: 7
Views: 4,698
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Forum: RNA Sequencing
10-15-2012, 07:35 AM
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Replies: 7
Views: 4,698
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Forum: RNA Sequencing
10-11-2012, 02:03 AM
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Replies: 7
Views: 4,698
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Forum: RNA Sequencing
06-08-2012, 08:17 AM
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Replies: 31
Views: 30,510
DNase treatment and fragmentation of RNA
Hi all,
I have recently started RNA extraction on different fish tissues with the aim of carrying out RNA-seq using Illumina Hi-seq.
Following a Trizol extraction protocol, I performed DNase...
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