User: Susmita Mandal

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Posts by Susmita Mandal

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Comment: C: coverage of a SNP site?
... Thank you so much. Now i get it :) ...
written 6 weeks ago by Susmita Mandal0
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coverage of a SNP site?
... Hey all, I have a doubt regarding what does it mean coverage at SNP sites. I'm supposed to be finding genes with SNPs ≥ 10X coverage in the samples and also they have taken average 8 SNPs/ transcripts. Any idea what it could mean. Thanks Susmita ...
bedtools ngs ase coverage snp written 6 weeks ago by Susmita Mandal0 • updated 6 weeks ago by Kevin Blighe33k
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Normalization of read counts from HTSeq by library size
... What does exactly this sentence means "**the total read counts from HTSeq were normalized by library size**"? I have gotten the read counts from HTSeq-count for all my samples. I don't know how to do the normalization of the total read counts by library size. Please help. Susmita ...
R htseq-count deseq2 ngs rna-seq written 8 weeks ago by Susmita Mandal0
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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 10 weeks ago by Susmita Mandal0 • updated 10 weeks ago by finswimmer8.2k
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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 10 weeks ago by Susmita Mandal0 • updated 10 weeks ago by finswimmer8.2k
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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 10 weeks 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 11 weeks 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 11 weeks 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 11 weeks 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 11 weeks ago by Susmita Mandal0 • updated 11 weeks ago by grant.hovhannisyan1.3k

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