User: cl10101

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cl1010180
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Posts by cl10101

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Comment: C: Comparing variants in vcf files that have been mapped to GRCh37 and GRCh38
... there is no output for 789016 ...
written 3.3 years ago by cl1010180
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Comment: C: Comparing variants in vcf files that have been mapped to GRCh37 and GRCh38
... Thank you for response. I removed char prefix in hg19ToHg38.over.chain file as you suggested and now I have error: "Exception in thread "main" htsjdk.tribble.TribbleException: Badly formed variant context at location chr1:789016; getEnd() was 789016 but this VariantContext contains an END key with ...
written 3.3 years ago by cl1010180
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Comment: C: Comparing variants in vcf files that have been mapped to GRCh37 and GRCh38
... Thank you. Unfortunately I can't find liftover chain file for g1k_v37 to hg38. I was trying to use hg19ToHg38.over.chain from http://hgdownload.soe.ucsc.edu/goldenPath/hg19/liftOver/ but output file is empty and all records were rejected. I found out that g1k_v37 is GRCh37 with slight differences. ...
written 3.3 years ago by cl1010180
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Comparing variants in vcf files that have been mapped to GRCh37 and GRCh38
... I have a VCF format file, which contains variants found for file mapped to hg38 (reference from GATK hg38 bundle) and I would like to compare this variants with VCF file from 1000 genome project, which is mapped to GRCh37. By comparing this files I mean finding variants shared by both files. Are the ...
vcf hg38 hg19 written 3.3 years ago by cl1010180 • updated 3.3 years ago by Pierre Lindenbaum129k
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Filtering VCF file by INFO flag
... I am trying to filter variants with dbSNP annotation. In my VCF file this information is contained in INFO column like this: Y 59003592 . A G . . NS=1;AN=1;AC=1;CGA_XR=dbsnp.96|rs2140187;CGA_SDO=2 GT:PS:FT:GQ:HQ:EHQ:CGA_CEHQ:GL:CGA_CEGL:DP:AD:CGA_ ...
vcf vcftools written 3.3 years ago by cl1010180 • updated 3.3 years ago by Pierre Lindenbaum129k
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BioMart dataset for S pombe
... Im trying to download TxDB from BioMart for Schizosaccharomyces pombe using: library(GenomicFeatures) library(biomaRt) makeTxDbFromBiomart(biomart ="fungal_mart" ,dataset="spombe_eg_gene" ,host="fungi.ensembl.org") but I get error message: Download and preprocess the 'transcripts' ...
s. pombe R biomart genomicfeatures bioconductor written 3.5 years ago by cl1010180 • updated 2.1 years ago by WouterDeCoster44k
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Comment: C: Characteristic features of Chip-seq and RNA-seq data
... Thank you for your response. I mapped my fastq files to reference genome and now I am trying to differentiate them visually using IGV. ![Samples mapped to genome][1] It seems to me that sample A (upper sample) has the most uneven coverage, but peaks location do not correspond to genes location (it i ...
written 3.5 years ago by cl1010180
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Characteristic features of Chip-seq and RNA-seq data
... What are the characteristic features of Chip-seq and RNA-seq data? If I have fastq files which are the results of Chip-seq and RNA-seq experiment is it possible to differentiate then, for example by comparing to Chip-seq input result, which is explicitly marked? ...
chip-seq rna-seq sequencing written 3.6 years ago by cl1010180 • updated 3.6 years ago by Carlo Yague5.0k
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Comment: C: GATK BaseRecalibrator - Input files knownSites and reference have incompatible c
... @HD VN:1.5 SO:unsorted @SQ SN:chr1 LN:248956422 M5:2648ae1bacce4ec4b6cf337dcae37816 UR:file:/home/user/ref/hg38.fa @SQ SN:chr10 LN:133797422 M5:907112d17fcb73bcab1ed1c72b97ce68 UR:file:/home/user/ref/hg38.fa @SQ SN:chr11 LN:135086622 M5 ...
written 3.6 years ago by cl1010180 • updated 3.6 years ago by WouterDeCoster44k
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Comment: C: GATK BaseRecalibrator - Input files knownSites and reference have incompatible c
... `$ grep "##contig" -m 10 dbsnp_144.hg38_with_chr.vcf` `$ grep "##contig" -m 10 ../ref/hg38.dict` `$ grep "##contig" -m 10 dbsnp_144.hg38_with_chr_sorted.vcf` `##contig=` `##contig=` `##contig=` `##contig=` `##contig=` `##contig=` `##contig=` `##contig=` `##contig=` `##contig=` ...
written 3.6 years ago by cl1010180

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