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Search: Posts Made By: Gorgon_VZ
Forum: Bioinformatics 01-09-2018, 09:27 AM
Replies: 5
Views: 1,774
Posted By Gorgon_VZ
You should be able to Check this by zoom in to...

You should be able to Check this by zoom in to nucleotide Level in igv. If the reads Do Not Match the reference this would be a Hind. I am Not a 100% Sure but i believe igv only uses the coordinates...
Forum: Bioinformatics 01-09-2018, 09:16 AM
Replies: 5
Views: 1,774
Posted By Gorgon_VZ
Hi! It could be an issue due to differing genome...

Hi! It could be an issue due to differing genome builds. Ich guess igv is using hg19 and reads are mapped to hg38.
Forum: Bioinformatics 01-03-2018, 03:49 AM
Replies: 3
Views: 1,414
Posted By Gorgon_VZ
Having a look on your FastQC figures I...

Having a look on your FastQC figures I recognised, that even before your trimming approach you have a huge number of short reads around 90bp (I guess the first figure shows the data before trimming...
Forum: Bioinformatics 01-03-2018, 03:11 AM
Replies: 2
Views: 2,362
Posted By Gorgon_VZ
Sorry the first explanation I posted was from...

Sorry the first explanation I posted was from bowties implemented command line help. The following description was actually taken from the manual:
--dpad <int>
“Pads” dynamic programming problems...
Forum: Bioinformatics 01-03-2018, 02:56 AM
Replies: 5
Views: 1,774
Posted By Gorgon_VZ
Hi! Is it really the exons only, that show...

Hi! Is it really the exons only, that show reduced coverage and the rest of the genome shows 40x? Have you checked the mean of all exons or for one particular gene only? What kind of genome and data...
Forum: Bioinformatics 01-03-2018, 01:42 AM
Replies: 3
Views: 3,507
Posted By Gorgon_VZ
Given the fact that issues can occur anywhere...

Given the fact that issues can occur anywhere beginning from samplequality,library-preparation, sequencing and last but not least parameter-settings used for assembly, it is hard to provide help with...
Forum: Bioinformatics 01-03-2018, 01:24 AM
Replies: 2
Views: 1,356
Posted By Gorgon_VZ
Hi, I just found a list of tools on this webpage...

Hi, I just found a list of tools on this webpage (http://www.metagenomics.wiki/pdf/definition/metatranscriptomics). Personally I only used Kraken so far, but actually Kraken only assigns taxonomic...
Forum: Bioinformatics 01-03-2018, 01:01 AM
Replies: 2
Views: 2,362
Posted By Gorgon_VZ
bowtie 2 dpad parameter explanation

Can someone provide a detailed explanation, what the bowtie2 parameter "--dpad" does? The explanation given in the manual is as follows: "--dpad <int> include <int> extra ref chars on sides of DP...
Forum: Pacific Biosciences 11-17-2016, 11:22 PM
Replies: 21
Views: 6,729
Posted By Gorgon_VZ
Hi all and thanks for your suggestions! I already...

Hi all and thanks for your suggestions! I already recognised pacBios Arabidopsis release. However, the Sequel-data comes in a "new" format (*.bam) and one needs to use smrt-link to visualise the...
Forum: Pacific Biosciences 11-10-2016, 02:15 AM
Replies: 21
Views: 6,729
Posted By Gorgon_VZ
Hi all, has anyone tested the performance of the...

Hi all, has anyone tested the performance of the novel chemistry yet? Any experiences regarding loading efficiency, readoutput, dataquality and so on? I would really, appreciate any kind of...
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