User: gerberd1990

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gerberd199020
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Posts by gerberd1990

<prev • 13 results • page 1 of 2 • next >
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Comment: C: Missing data calling (I know, sounds weird...)
... Hi, thank you for your help :) Seems useable ...
written 23 months ago by gerberd199020
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Missing data calling (I know, sounds weird...)
... Hi everyone, I am working with ancient DNA, and I'd like to call a consensus fasta file from my mapped data (BAM). Since it is ancient DNA it is often happening that there are missing, or poorly covered positions in my BAMs, so when I want to call a consensus fasta from vcf I also want to call the m ...
sequence snp written 23 months ago by gerberd199020
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BAM to FASTA with uncovered regions
... Dear All! I work on archaic DNA (mitochondrial in this case), and due to the aDNA's nature, the final assembly has gaps in it. I have BAM files and I want to convert them to FASTA, so I used samtools fasta command for it, but then I got multiple FASTA's per a single BAM, one FASTA one for one covere ...
genome sequence next-gen written 2.3 years ago by gerberd199020
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Comment: C: Mixed PE and SE reads
... first question: I merged the R1 and R2 reads to a single file and I treated them as one file with SE reads second question: when I merge the reads, about 10-50% of them filtered out due to the lack of enough overhanging bases. It is because the with cycle 50 run we had got too much non-overhang read ...
written 2.7 years ago by gerberd199020
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Mixed PE and SE reads
... Hi all, I have a weird situation here: I am working with archaic DNA (aDNA) reads, and we had a few sequencing run in the past weeks. The cycle number was set to 50-100 (each run had its own cycle number), but some of the samples were the same (in this case I merged the fastq files to a single R1 an ...
assembly next-gen alignment written 2.8 years ago by gerberd199020
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(Closed) Illumina sequencing fail
... Hi everyone, a few days ago we had a MiSeq run, but it failed for some reasons. My job was to find out what was the problem, but I had never been working with MiSeq run data before, so I need a little help. I have that first (and very strong) assumption, that the dispersion of the DNA solution on th ...
next-gen sequencing written 2.8 years ago by gerberd199020
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Comment: C: What is the difference between BWA and de Bruijn graphs?
... Thank you very much! :) ...
written 2.8 years ago by gerberd199020
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What is the difference between BWA and de Bruijn graphs?
... Hi all, I know this might be a very stupid question, but I have confused about the read assembling methods and their usage. I know (sort of) how does the BWA works independently, and also how does the de Bruijn graphs works independently, but I do not know, when and why does the assembler softwares ...
genome assembly alignment written 2.8 years ago by gerberd199020 • updated 2.8 years ago by Tonor420
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Comment: C: BWA mapping - only mapped the part of the reads, why?
... It was just when I posted it, my filenames are far different from these :) ...
written 3.0 years ago by gerberd199020
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Comment: C: BWA mapping - only mapped the part of the reads, why?
... bwa aln reference.fasta sample_merged_barcode/adapter-trimmed_.fastq > sample.sai bwa samse reference.fasta sample.sai sample_merged_barcode/adapter-trimmed.fastq > sample_SE.sam As you can see, the reads were previously quality and adapter trimmed (with cutadapt), and merged with lee ...
written 3.0 years ago by gerberd199020 • updated 3.0 years ago by Devon Ryan91k

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