User: Sammy

gravatar for Sammy
Sammy10
Reputation:
10
Status:
New User
Location:
United Kingdom
Website:
https://ruxseq.uk/
Last seen:
23 hours ago
Joined:
1 year, 11 months ago
Email:
r*********@gmail.com

Posts by Sammy

<prev • 46 results • page 1 of 5 • next >
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Comment: C: Bacterial RNA-SEQ - Quality Control
... I'm thinking of asking the sequencer provider for the adapters he used. Would that be a good idea? Maybe that's the problem. I checked [in here][1] but who knows. [This][2] was a source of inspiration. [1]: https://thesequencingcenter.com/wp-content/uploads/2019/04/illumina-adapter-sequences.pd ...
written 1 day ago by Sammy10
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Comment: C: Bacterial RNA-SEQ - Quality Control
... Hi GenoMax, I have run Trimmomatic (operation: SLIDINGWINDOW, Number of bases to average across: 4, Average quality required: 20) on some of my samples and done the FASTQC again. The Per Sequence GC content is not much different. Do you have any suggestions? Or how should I approach this issue? ...
written 2 days ago by Sammy10 • updated 2 days ago by GenoMax96k
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Comment: C: Bacterial RNA-SEQ - Quality Control
... I mean L001_R1 "per sequence GC content" looks identical with L002_R1, L003_R1 and L004_R1. Ok, so that looks alright then? What about 2 peaks? I read that's a sign of contamination but again, the quality score is good even then? ![enter image description here][1] ![enter image description here][2] ...
written 6 days ago by Sammy10 • updated 6 days ago by GenoMax96k
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Bacterial RNA-SEQ - Quality Control
... Heyya, Trying to figure out Quality Control for RNA-SEQ. I ran FASTQC on the first batch and the same sample, forward strand looks the same as on each lane. The same with the reverse. Is this normal? Plus it looks kind of like this: ![I have a huge peak on per sequence GC content][1] ![enter ima ...
rna-seq written 6 days ago by Sammy10 • updated 6 days ago by swbarnes29.6k
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Comment: C: Bacterial (E.coli) RNA-SEQ differential gene expression (with pET system)
... Hi Joe. Thank you for your response. I am aware the comparison might be tricky based on those experimental conditions. However, personally, I am more interested in the list and read depth of all expressed genes for each bacterial construct. This can't be that noisy, can it? Yes, the plasmid has t ...
written 6 days ago by Sammy10
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Bacterial (E.coli) RNA-SEQ differential gene expression (with pET system)
... Heyya, I have some bacterial RNA-SEQ data to analyse. The goal is to get a list and read depth of all expressed genes. I have 5 different experimental conditions (in triplicate). 1. Although there is the same bacterial strain, a pET system has been used. In each experimental condition, there is a ...
rna-seq written 6 days ago by Sammy10 • updated 6 days ago by Joe19k
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Comment: C: Lanes in the context of RNA-SEQ data
... Thank you, GenoMax :) ...
written 7 days ago by Sammy10
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Comment: C: Lanes in the context of RNA-SEQ data
... Sorry. The sequencer provider told me they ran on a NextSeq 550 2x 75bp high output kit. The library prep was done with NEB Ultra II Directional RNA Library Prep Kit for Illumina® . I expressed myself poorly. ...
written 8 days ago by Sammy10
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Comment: C: Lanes in the context of RNA-SEQ data
... Thank you. They were in fact on a NextSeq (looked into the library prep) and, indeed, all samples were prepared in triplicate. So a1_L001.fastq.gz a1_L002.fastq.gz a1_L003.fastq.gz a1_L004.fastq.gz should be the same sample. :) ...
written 8 days ago by Sammy10
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Comment: C: Lanes in the context of RNA-SEQ data
... That was really useful. Now I definitely have a starting point. Is it plausible that lanes, in this case, separate different experiments? I was not involved in biological experiments or sequencing. I'm working with what I have. (I couldn't post any comment for a few hours and I had to wait) Cheers ...
written 8 days ago by Sammy10

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