User: abedkurdi10

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abedkurdi1030
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Posts by abedkurdi10

<prev • 37 results • page 1 of 4 • next >
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Answer: A: RNA-seq Infer experiment wrong strandeness information
... It seems that there is more rRNA sequences. I downloaded `rmsk` bed file from UCSC and removed all reads covering those Repeating Elements (including and not limited to rRNA, tRNA...), then I run again `infer_experiment` and everything went well. ...
written 6 weeks ago by abedkurdi1030
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Comment: C: RNA-seq Infer experiment wrong strandeness information
... I will have a look on them. Actually, It's mouse data. ...
written 6 weeks ago by abedkurdi1030
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RNA-seq Infer experiment wrong strandeness information
... Hello everyone, I have received recently eight RNA-seq samples. We know that the reads are `reversely stranded`. After aligning those samples to their reference genome, I run `infer_experiment` on the alignment data just to make sure everything is fine. Five samples out of eight showed that they ...
infer_experiment rna-seq rseqc written 6 weeks ago by abedkurdi1030
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Comment: C: Interval list for GATK tool Haplotype Caller
... Yes, for every gene or for genes of interest ...
written 8 weeks ago by abedkurdi1030
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Answer: A: Interval list for GATK tool Haplotype Caller
... As I know, intervals in HaplotypeCaller are BED files (Genomic positions). You specify the regions where to call variants. ...
written 9 weeks ago by abedkurdi1030
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Comment: C: Conversion of Vep.vcf to MAF format?
... but this is the same vcf2maf.pl which requires vep to run ...
written 11 weeks ago by abedkurdi1030
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Comment: C: Conversion of Vep.vcf to MAF format?
... Maybe you can use `bcftools +split-vep` and extract the variants in tabulated format with specific order of the fields. ...
written 11 weeks ago by abedkurdi1030
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Answer: A: Conversion of Vep.vcf to MAF format?
... While it is no more maintained, but try this: `https://github.com/cbare/vcf2maf` ...
written 11 weeks ago by abedkurdi1030
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Comment: C: Bigwig circular plot
... Thank you for your suggestion. Actually, I am looking for interactive plots rather than static ones, like zooming in and out, moving tracks... ...
written 3 months ago by abedkurdi1030
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Bigwig circular plot
... Hello all, Does anyone knows about representing BigWig in a circular plot? Any tool or library especially in JavaScript that can be used to represent BigWig files? I appreciate the suggestions, Thank you ...
plotting java bigwig tool javascript written 4 months ago by abedkurdi1030 • updated 4 months ago by Pierre Lindenbaum129k

Latest awards to abedkurdi10

Popular Question 6 months ago, created a question with more than 1,000 views. For raw data (fastq files) of whole exome sequencing (WES) of somatic mutations
Popular Question 3.5 years ago, created a question with more than 1,000 views. For raw data (fastq files) of whole exome sequencing (WES) of somatic mutations
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Thresholds to filter out variants from vcf file
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Clinical significance explanation
Popular Question 3.5 years ago, created a question with more than 1,000 views. For VCF file re-header

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