User: va90

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va9010
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Posts by va90

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How to determine the origin of child's SNVs in trios?
... Hi, Is there any tool that accepts vcf files for child, father, and mother (trio) and then imputes the origin of variants in the child (whether it stem from mother, father, or both)? Many thanks, Vahid. ...
genome snp sequencing written 6 weeks ago by va9010
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Is there any database or study to get the list of known imprinting control regions for Human?
... Hi everyone, I was wondering, is there any database or study which gathered the list of known imprinting control regions and their genomic positions in Human? I could find the list of known imprinted genes from [this source][1], but I need to know the ICR that controls those imprinted genes. ...
genome imprinting written 8 weeks ago by va9010
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How to get inserted bases using pysam pileup
... Hi, I am using pysam.pileup to get the base per information from a bam file. I am using the following code: import pysam samfile = bamfh=pysam.AlignmentFile(bam_file,'rb') def get_base_info(samfile,chrom,pos,map_qual): for pileupcolumn in samfile.pileup( chrom, pos, pos+1, trunc ...
next-gen alignment pysam bam written 11 weeks ago by va9010 • updated 9 weeks ago by Biostar ♦♦ 20
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How to download oxford nanopore sequencing fast5 files from SRA
... Hi, I am trying to download direct RNA seq data produced by oxford nanopore sequencing from SRA ([SRP174366][1]). I know how to use sratoolkit prefetch or fastq-dump to download fastq files, but I do not know how to download nanopore fast5 files from SRA? Any help would be much appreciated, Thank ...
rna-seq written 8 months ago by va9010 • updated 8 months ago by genomax87k
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Comment: C: How to get the position of a single base in a sequencing read in respect to the
... Hi @Pierre Lindenbaum, I had a question regarding this software. Does it consider the + or - strand? and if I want to combine the extracted results of this software with a bed file which has positions based on + and - strand, how can I do that? I would be grateful if you could instruct me with t ...
written 11 months ago by va9010
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Comment: C: How to get the position of a single base in a sequencing read in respect to the
... Thank you, @Pierre Lindenbaum. It seems this tool can satisfy my need. Many Thanks, Vahid. ...
written 11 months ago by va9010
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How to get the position of a single base in a sequencing read in respect to the reference
... Hi, I have a bam file generated from analysis of nanopore data. I also have another file which includes the read IDs and the position of cytosine bases that predicted to be methylated. Now, I want to find the position of that methylated cytosines in the reference genome. Let say I have a read nam ...
sequencing written 11 months ago by va9010 • updated 11 months ago by juanjo75es70
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Comment: C: Affymetrix Microarray Between-array normalization
... Thank you so much, Kevin ...
written 14 months ago by va9010
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Comment: C: Affymetrix Microarray Between-array normalization
... Hi Kevin, Thank you so much for your response, I am using this data "GSE61723". I have already downloaded the data using the method you mentioned. But if you see these plots [click here](https://ibb.co/qr77kzv), [click here](https://ibb.co/9HTbPPD), [click here](https://ibb.co/4MJVV39), [click ...
written 14 months ago by va9010
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Affymetrix Microarray Between-array normalization
... Hi all, I would be grateful if someone could help me with my question. I have downloaded GEO Series Matrix data using GEOquery. When I look at box plots and density plots it looks my data needs between-array normalization which I want to do by Limma using "normalizeBetweenArrays". I wanted to ...
R written 14 months ago by va9010

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