User: natarajan.padmaja

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Posts by natarajan.padmaja

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How many gene transcripts are there in Rat genome (latest assembly)?
... I am working on an RNA-Seq project with sequencing data from Rat samples. I would appreciate some help with obtaining the latest list of Rat (Rattus-norvegecus) transcripts (FASTA file). It appears that Rat genome (Rnor_6.0 assembly) has about 41,000+ gene transcripts as opposed to over 135,000+ M ...
assembly rna-seq written 12 days ago by natarajan.padmaja10 • updated 5 days ago by luxeredias10
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How to get a VCF file for all variants in a specific gene and specific exon?
... How to get a VCF file for all variants (single nucleotide variants, insertions/deletions, copy number variants and structural variants) from reference genome (e.g. GRCh38) for a specific gene (e.g. BRCA1) and in specific exon (e.g. 10) ? Thanks. ...
vcf bed snp written 19 months ago by natarajan.padmaja10
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Over-hang penalty in alignment process
... I am a new user of bbmap. I am trying to align short reads to reference sequence of 1200 bases and I would like have NO penalty for the overhangs on either ends to my reference sequence, but otherwise normal penalties (for mismatch, etc) within the reference sequence. Are there specific parameters o ...
alignment bbmap written 21 months ago by natarajan.padmaja10 • updated 21 months ago by genomax46k

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