User: SemiQuant

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SemiQuant70
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South Africa
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Posts by SemiQuant

<prev • 38 results • page 1 of 4 • next >
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Comment: C: snpEFF chr not found error bacterial genome
... see below, you can just change it in your vcf file, or in the fasta you used to generate the database. (also see [here][1]) [1]: https://pcingola.github.io/SnpEff/SnpEff_faq.html#ERROR_CHROMOSOME_NOT_FOUND ...
written 6 months ago by SemiQuant70
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Bacterial population reconstruction
... Hi, I am doing amplicon sequencing (100 000x) on several targets of a bacteria. I expect most of the cultures to be clonal, however, there will be instances of heterogeneous populations. I want to, using the pair-end short-read sequencing, determine the haplotypes fo the bacteria present. I first w ...
haplotype population phase phasing written 7 months ago by SemiQuant70
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Answer: A: Trimming fastq up until a sequence
... I've fount that [filtlong has a trim][1] option that also does this. [1]: https://github.com/rrwick/Filtlong#trimming-and-splitting ...
written 13 months ago by SemiQuant70
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Comment: C: Trimming fastq up until a sequence
... I can't believe I missed that in the guide (its the first paragraph!) Thanks. ...
written 13 months ago by SemiQuant70
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Trimming fastq up until a sequence
... Hi I have a somewhat difficult problem to find a solution to on google. I need to trim my fastq files up until a sequence, and not remove that sequence (but remove everything before it). This someRandomNoise_aKnownSequence_unknownSequence becomes aKnownSequence_unknownSequence A ...
trimming fastq sequencing written 13 months ago by SemiQuant70
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Comment: C: UMI read consensus calling
... Thanks, but Cablib can only deal with pair-end reads (I wasn't clear in my initial question) so I cant use it without a lot of customization (or maybe I can filter by length and then just split the fatqs?). I hope you get the funding to implement it in UMI-tools; I'm sure it would be used a lot with ...
written 13 months ago by SemiQuant70
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UMI read consensus calling
... Hi I have amplicon sequence data where I included a UMI (unique molecular identifier) on my reads to allow me to correct sequencing errors. I have removed the UMIs from the reads and added them to a tag in the fastq files. I have then aligned the reads to my reference and would now like to make con ...
umi next-gen unique molecular identifier nanopore written 13 months ago by SemiQuant70 • updated 13 months ago by i.sudbery11k
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Answer: A: Subset (reduce) bam to contain only variant containing reads
... I don't know why Pierre Lindenbaum answer doesn't show but he proposed this solution. samtools view -h in.bam | grep -E '^@|NM\:i\:[^0]' > out.sam NM:i:count = Number of differences (mismatches plus inserted and deleted bases) between the sequence and reference... If it's missing you can a ...
written 14 months ago by SemiQuant70
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Comment: C: how to extract allele specific reads from bamfiles?
... This is really helpful. It would be great if you could opt out of giving the allele and it would just mark non-reference cases. ...
written 14 months ago by SemiQuant70
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Subset (reduce) bam to contain only variant containing reads
... I have targeted sequencing alignments bam files. I want to "pull out" only read pairs in which the reads have a variant, i.e. do not perfectly match the reference. It doesn't matter if these are sequencing errors etc. Any suggestions, simply using samtools would be great but I could find any bam fl ...
alignment samtools bam sequencing written 14 months ago by SemiQuant70

Latest awards to SemiQuant

Epic Question 5 months ago, created a question with more than 10,000 views. For Addin gene information to VCF file
Great Question 11 months ago, created a question with more than 5,000 views. For Addin gene information to VCF file
Scholar 2.9 years ago, created an answer that has been accepted. For A: snpEFF chr not found error bacterial genome
Great Question 3.7 years ago, created a question with more than 5,000 views. For Addin gene information to VCF file
Popular Question 3.7 years ago, created a question with more than 1,000 views. For Bacterial GWAS analysis?
Popular Question 4.4 years ago, created a question with more than 1,000 views. For Bacterial GWAS analysis?
Popular Question 4.6 years ago, created a question with more than 1,000 views. For GATK variant recal malformed vcf
Popular Question 5.1 years ago, created a question with more than 1,000 views. For Addin gene information to VCF file
Popular Question 5.3 years ago, created a question with more than 1,000 views. For Addin gene information to VCF file

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