User: Mick

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Mick10
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Posts by Mick

<prev • 9 results • page 1 of 1 • next >
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Answer: A: Find all perfect matches for short sequences to human reference genome
... Thank you guys so much for all the replys. I tried bowtie and used these parameters: bowtie hg19 -v 0 -a -X 800 -r1 "sequences1.txt" -r2 "sequences2.txt" It worked really well for the most part. It only missed a couple of primers, where it didn't find any alignment. I manually searched for the loc ...
written 6 weeks ago by Mick10
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Comment: A: Find all perfect matches for short sequences to human reference genome
... Thank you for the quick reply, I'll let you know how it works :) ...
written 6 weeks ago by Mick10
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Find all perfect matches for short sequences to human reference genome
... Hi guys, I'm trying to get something done that sound super simple but I'm stuck and I don't know how to go about it. I have a large excel file with Primer sequences that someone designed for the human genome and I need to find out which part of the genome they cover. All i have is the sequence for ...
alignment written 6 weeks ago by Mick10
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Comment: A: Illumina Overlapping R1/R2 reads, error-correction in python
... I set out to try and recreate what our bioinformatician does, but since I do not have a step by step instruction I need to get creative here and there. Well its not really paired end data in the usual sense right?, because its actually completely the same genomic region just in reverse. There is no ...
written 4 months ago by Mick10
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Comment: A: Illumina Overlapping R1/R2 reads, error-correction in python
... I use bwa for the alignment. Can I align both files for forward and reverse read with the option "single-end" and then join the bam files or should I use "paired-end". Is there any advantage using paired-end for my purposes? ...
written 4 months ago by Mick10
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Comment: A: Illumina Overlapping R1/R2 reads, error-correction in python
... This approach has been in use in our lab for a while now. I'm a med student and usually my job is the library preparation in the lab. I'm trying to figure out how the data analysis part works because I would like to be able to take a look at the data myself and draw my own conclusions, but our bioin ...
written 4 months ago by Mick10
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Comment: A: Illumina Overlapping R1/R2 reads, error-correction in python
... Hi genomax, we have barcodes on the outside of the read which we use to seperate the samples. I have already dealt with that with the tool cutadapt. It worked well, I didn't have any problems there. So the samples are already seperated into their own fastq files for F and R read. The UMIs are rando ...
written 4 months ago by Mick10
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Comment: A: Illumina Overlapping R1/R2 reads, error-correction in python
... Hey guys, thank you for your input. Ok so my sequencing data may be a bit unique. I have around 1 million reads per sample. All from the same 100bp genomic region. I'm looking for a rare SNP mutation at one specific base of that region (say 0.1% of the reads have the mutation at that position). The ...
written 4 months ago by Mick10
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Illumina Overlapping R1/R2 reads, error-correction in python
... Hi guys, I'm new to this community. I have two fastq files per sample from our Illumina platform with the forward and reverse reads. I cut the reads in both files so that only the segment in the middle where the two reads overlap is left ( around 100bp). I would like to use forward and reverse read ...
alignment sequence snp written 4 months ago by Mick10

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