User: a.hasankhani74

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Posts by a.hasankhani74

<prev • 25 results • page 1 of 3 • next >
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mapping status for each region
... Hi. I have bam file from hisat2 aligner in RNA-seq data analysis.I used from samtools flagstat for mapping status but I want percentage of reads mapped to each region separately. how to generate The percentage of reads mapped to exonic, intronic and intergenic regions. ...
rna-seq written 6 months ago by a.hasankhani740
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SNP type percentage in vcf
... Hi I have a vcf file contained SNPs. how can I obtain SNP type percentage and plot them from vcf file ? ...
snp rna-seq written 7 months ago by a.hasankhani740
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Variant annotation tools
... hi Is there software for SNP annotation instead of snpEff? how can I plot my vcf file? ...
snp written 7 months ago by a.hasankhani740 • updated 7 months ago by Kevin Blighe60k
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Comment: C: obtain common SNPs
... how can I merge them? and how can I filter them for those positions that for both samples have been called? Are you have pipeline for these? ...
written 7 months ago by a.hasankhani740
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Comment: C: obtain common SNPs
... SNPs in each file was 11350. If I want to look for each position It's time-consuming. I'm looking for the fastest way I can. ...
written 7 months ago by a.hasankhani740
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snpEff Apis_mellifera genome
... Hi I have a problem with snpEff genome. I want to obtain snp annotation with snpEff. my organism is Apis_mellifera. I run snpEff with below command. java -jar snpEff/snpEff.jar -c snpEff/snpEff.config -v Apis_mellifera New\ folder/Ligustica_snp.vcf > New\ folder/Ligustica_ann.vcf ...
software error rna-seq snp written 7 months ago by a.hasankhani740 • updated 7 months ago by colindaven2.2k
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obtain common SNPs
... Hi I have two vcf file from two treatment. how can I obtain common snp from this two vcf file? ...
rna-seq written 7 months ago by a.hasankhani740
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Comment: C: SNP Discovery error
... give your email address or skype ID to me.I want to speak with you for this subject ...
written 7 months ago by a.hasankhani740
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Comment: C: SNP Discovery error
... here you are: ``` 1 216982 225458 JUNC00000001 3 ? 216982 225458 255,0,0 2 64,71 0,8405 1 216983 225404 JUNC00000002 1 + 216983 225404 255,0,0 2 63,17 0,8404 1 225527 225753 JUNC00000003 7 ? 225527 225753 255 ...
written 7 months ago by a.hasankhani740 • updated 6 months ago by RamRS27k
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Comment: C: SNP Discovery error
... no.head of bowtie-inspect. the junction.bed is symphonic with cat command. the source of problem is in genome file obtained from bowtie-inspect.but I cant solve it. ...
written 7 months ago by a.hasankhani740

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