User: Susmita Mandal

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Posts by Susmita Mandal

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Comment: C: intersectBed a gtf file with a vcf file
... This command seems to give me same results in all the samples: intersectBed -a /home1/Mouse_Reference_genome/NCBIM37.67/Mus_musculus.NCBIM37.67_plus.gtf -b /home1/temp/8/8_SRR_133_forward_intersect.vcf > /home1/Intersect_by_GTF/plus/SRR_133_plus.gtf The gtf files are identical! And this co ...
written 12 days ago by Susmita Mandal0 • updated 12 days ago by finswimmer6.2k
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Comment: C: intersectBed a gtf file with a vcf file
... ##fileformat=VCFv4.2 #CHROM POS ID REF ALT QUAL FILTER INFO 129S1 JF1 1 3000176 . T G 40.00 PASS . 0 0 1 3000223 . T A 40.00 PASS . 0 0 1 3000248 rs32640266 G T 237.81 PASS . 0 0 1 3000289 rs32137367 T G 255.31 PASS . 0 0 ...
written 12 days ago by Susmita Mandal0 • updated 12 days ago by finswimmer6.2k
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intersectBed a gtf file with a vcf file
... Hey all, I have been trying to intersect a gtf file with a vcf file using intersectBed without using any options. I have edited my VCF, it has the 8 necessary fields and I have added two columns of my own which are read counts from bed files when intersected with a vcf file ( intersectBed -c ). And ...
bedtools intersectbed snp written 12 days ago by Susmita Mandal0
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Comment: C: Reads that map to two different genomes, but with different map coordinates
... The reference genome is same acting as a template and the SNPs are being incorporated into it from two mouse strains to make two pseudo genomes. ...
written 20 days ago by Susmita Mandal0
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Reads that map to two different genomes, but with different map coordinates
... Hello everybody, I have samples that I have mapped onto two custom pseudo genomes using STAR, thus creating two SAM/BAM files per sample. A small number of reads may be mapped with numerous or abnormal splice sites, or soft clipped reads mapped to different locations due to the presence of homologo ...
ngs bam bamutil comparison bamutil diff written 20 days ago by Susmita Mandal0
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Comment: C: Allele Specific Expression Analysis
... I do not have single cell RNA Seq data. But I'll look into the ASEReadCounter of GATK for sure! ...
written 23 days ago by Susmita Mandal0
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Allele Specific Expression Analysis
... Hey All, Does anyone have any experience in Allele specific gene expression analysis? Any recommended tools and pipelines? And any idea on how to retain only RNA-seq reads overlapping known SNP sites that differ between the two distinct parental genomes? I have fair knowledge of RNA Seq and SNP ana ...
x chromosome snp star rna-seq allele specific written 23 days ago by Susmita Mandal0 • updated 23 days ago by grant.hovhannisyan1.1k
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Comment: C: vcf-consensus outputs sequence same as reference
... Did you figured out what it was? Coz I'm struggling with the same. ...
written 27 days ago by Susmita Mandal0
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Comment: C: LiftOver a VCF file
... I am creating custom in silico parental genomes and for that i would need VCFs from both the parents mapped onto the same reference genome ...
written 28 days ago by Susmita Mandal0
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Comment: C: LiftOver a VCF file
... I took your advice. Earlier I couldn't find VCFs of 129S1/Sv mapped onto mm9. I found some files though last night, its a tab delimited file with #CHROM POS REF 129S1/Sv and a tbi file. I have no idea how to get the vcf file from these two. Any ideas? ...
written 28 days ago by Susmita Mandal0

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