User: ja4123

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ja41230
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Posts by ja4123

<prev • 24 results • page 1 of 3 • next >
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Comment: C: bedtools intersect usage problem
... I will try that. Thanks for help! ...
written 29 days ago by ja41230
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Comment: C: bedtools intersect usage problem
... It is possible to get list of genes (gene id) in which peaks fall into? ...
written 29 days ago by ja41230
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Comment: C: bedtools intersect usage problem
... Thanks for the answer! Could you explain to me what is the output from the command you wrote and if it is possible to store it in .bam file or any other file? ...
written 29 days ago by ja41230
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bedtools intersect usage problem
... Hello! I need to filter peaks which are withwin gene regions. I have .bam file from CHIP-seq experiment and .bam file from RNA-seq. I am trying to do this with this command: bedtools intersect -a A.bam -b B.bam > AB.bam The problem is that the output AB.bam is exactly the same as A.bam (it i ...
bedtools intersect bam written 29 days ago by ja41230 • updated 29 days ago by i.sudbery11k
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Files for CHIPseeker analysis
... Could someone please explain to me what files I need to have to do the CHIPseeker analysis? For example: peakAnno <- annotatePeak(files[[4]], tssRegion=c(-3000, 3000), TxDb=txdb, annoDb="org.Hs.eg.db") What is that txdb file? I understand I have to annotate .bed file I have first? Kindl ...
chipseeker chip-seq R written 6 weeks ago by ja41230
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Location of the peaks from CHIP-seq data in the genome
... Hey! I have CHip-seq data from two experiments. I have created bam files frist, then using macs3 I've made .bed and .narrowPeak. I need to examine the location (introns, exons, promoters, centromers and so on) and the number of peaks in genome. Can someone suggest the tool for that? Kindly help. ...
chip-seq macs3 narrowpeak bed written 6 weeks ago by ja41230
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How to convert vcf.bgz to vcf.gz?
... I am looking for some quick way to convert vcf.bgz to vcf.gz, any advise? Thanks in advance for the help. ...
vcf bgz gz gnomad written 13 months ago by ja41230 • updated 3 months ago by Biostar ♦♦ 20
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How to read vcf file in python?
... When I try to do simply like this: import vcf vcf_reader = vcf.Reader(filename="in.vcf.gz") there is an error: AttributeError: partially initialized module 'vcf' has no attribute 'Reader' (most likely due to a circular import) But vcf module has that attribute .. Kindly help. ...
vcf python reader written 13 months ago by ja41230 • updated 13 months ago by onestop_data270
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Comment: C: Problem succesfully running freebayes
... Okey, so any advise which file has to bo modified and which way? ...
written 13 months ago by ja41230
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Comment: C: Problem succesfully running freebayes
... gunzip -c in.vcf.gz | grep -v '# ' | cut -f 1 | uniq output are metadata from vcf and column #CHROM, that is: chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY chr1_KI270706v1_random chr4_GL000008v2_random chr7_K ...
written 13 months ago by ja41230

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Popular Question 4 weeks ago, created a question with more than 1,000 views. For How to read vcf.bgz or vcf.gz in python using PyVcf?
Popular Question 13 months ago, created a question with more than 1,000 views. For How to read vcf.bgz or vcf.gz in python using PyVcf?
Popular Question 13 months ago, created a question with more than 1,000 views. For HISAT2 Error: Encountered internal HISAT2 exception (#1)
Popular Question 13 months ago, created a question with more than 1,000 views. For How to read vcf file in python?

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