User: ambi1999

gravatar for ambi1999
ambi199930
Reputation:
30
Status:
New User
Location:
United Kingdom/Cardiff/Cardiff Metropolitan University
Website:
http://www.cardiffmet....
Twitter:
ambi1999
Last seen:
4 months, 3 weeks ago
Joined:
2 years, 6 months ago
Email:
a*******@gmail.com

Interested in analysing next generation sequencing data.

Posts by ambi1999

<prev • 19 results • page 1 of 2 • next >
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Split oxford nanopore MinION fastq file based on barcode
... Hi, How can I split a single fastq file into multiple fastq file based on barcode in the header of reads? I got a single oxford nanopore MinION fastq file containing reads from multiple samples. Each read has a barcode in header identifying the sample. For example as follows. @7a68bd87-67c2- ...
barcode fastq minion oxford nanopore minion split written 4 months ago by ambi199930 • updated 4 months ago by WouterDeCoster37k
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Comment: C: Inverse mutation: Is Mummer output conclusive proof of inversion
... I did it but it is not being displayed in the question text. Here is the link https://ibb.co/cQucnx ...
written 12 months ago by ambi199930
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Inverse mutation: Is Mummer output conclusive proof of inversion
... Hi, I am trying to find if there is inversion happening between two bacterial samples. I did the denovo assembly for the samples and then compared the assemblies using Mummer. Below is the graph that I got from Mummer. Please note that -r was used while running mummer so that only reverse compleme ...
mummer mutation inverse mutation inversion written 12 months ago by ambi199930
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Comment: C: Bacterial sequence reads supporting two nucleotides at same location
... Hi Brian, >You have several of nearby SNPs, within read length, which is convenient; and they all seem to share phase. What you mean by share phase? Do you mean these are on the same scaffold? How does it matter if snps are on same scaffold? My understanding is that Phased vs unphased is relev ...
written 2.0 years ago by ambi199930
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Comment: C: Bacterial sequence reads supporting two nucleotides at same location
... Thx Brian. Here are the zoomed out versions. Zoomed out version for location 401 ![enter image description here][1] Zoomed out version for location 942 ![enter image description here][2] There are nearby variants which are listed below. So I think SV/misassembly is still a possibility? Please ...
written 2.0 years ago by ambi199930
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Comment: C: Bacterial sequence reads supporting two nucleotides at same location
... Hi Brian, >And then, there are the weird ones, with perhaps 40% of the reads indicating a variant. Sometimes this is due to Illumina platform-specific sequencing error. You can often determine this by looking at the location in IGV and seeing that the variant is only present in reads on the plus ...
written 2.0 years ago by ambi199930
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Comment: C: Bacterial sequence reads supporting two nucleotides at same location
... Hi jrj.healey, Thanks for your reply. Due to the unstable nature of the small colony variants we had to use more than one colony for each isolate, which means that even though we used a pre culture, because we used several colonies there might be some clonal variation within that pure culture. So ...
written 2.1 years ago by ambi199930
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Comment: C: Denovo assembly SPAdes ERROR K-mer Counting: too many k-mers to fit into availab
... just accepted the answer. Thx again for your help. Ambi. ...
written 2.1 years ago by ambi199930
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Comment: C: Bacterial sequence reads supporting two nucleotides at same location
... Hi Brian, Thx. Any recommendation for SV caller? The samples are mutated forms of bacteria (Pseudomonas aeruginosa). Ambi. ...
written 2.1 years ago by ambi199930
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Comment: C: Bacterial sequence reads supporting two nucleotides at same location
... I meant its not a one off scenario. I have not counted but there are more than 100 such locations. Ambi. ...
written 2.1 years ago by ambi199930

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