User: inayat45shaikh

Reputation:
40
Status:
New User
Location:
India
Last seen:
1 month ago
Joined:
5 years ago
Email:
i*************@gmail.com

Posts by inayat45shaikh

<prev • 13 results • page 1 of 2 • next >
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difficulty in executing micropred
... I am trying to run micropred for feature assessment from microRNA sequences, but getting following error [inayat@gibhpc1 progs]$ perl microPred.pl seq.fasta -microPred started... -calculating features------------- -folding original sequences... -calculating miPred sequential ...
rna-seq written 11 months ago by inayat45shaikh40 • updated 11 months ago by genomax67k
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How to predict amino acid sequence after a framshift deletion in the gene
... Hello group, I want to predict amino acid sequence of gene after deleting a single nucleotide? ...
next-gen sequence snp written 2.3 years ago by inayat45shaikh40 • updated 2.3 years ago by willgilks260
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Answer: A: Somatic and Germline variant calling in ion torrent
... Thanks Sean, for the response..... can you suggests some software's I have a question, are these softwares takes input raw files or aligned bam files, i dont know about the idea of calling variants from tumor and normal raw files, but i do know little bit about calling variants from aligned bam fil ...
written 2.9 years ago by inayat45shaikh40
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Need clarity on the concept of germline mutations
... Hello everyone I am analyzing some cancer samples wherein I have mutations have been detected from normal blood sample and tumor tissue sample of the same patient. Now I am getting mutation that are present in normal but not in tumor sample. What kind of mutation is this?? As far as i know germline ...
genome next-gen snp sequencing written 3.4 years ago by inayat45shaikh40 • updated 3.2 years ago by michael.d.mclellan140
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Somatic and Germline variant calling in ion torrent
... Hello, We have data of tumor (Tissue) and Normal (Blood) control from the same patients. We want to call somatic and germline variants in the same individual. To achieve this, We aligned Tumor and normal sample each separately with hg19 and called variants. For identification of somatic mutations, ...
alignment snp written 3.4 years ago by inayat45shaikh40 • updated 2.8 years ago by graeme.grimes10
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How to annotate SNPs, identified against scaffolds (draft genome)
... Hello group, I had identified SNPs by mapping reads to scaffolds (closely related organism) and generated VCF file. The problem I am facing is in annotation. I wanted to classify these variants into exonic, intronic, synonymous, non-synonymous etc. I came across some SNP annotation pipelines I.e. v ...
snp written 3.5 years ago by inayat45shaikh40 • updated 3.5 years ago by Sean Davis25k
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Comment: C: What should be the minimum percent of identity and coverage of blast hits for co
... Thanks for the above paper. Paper is stating, e-values and bit scores (bits > 50) is more sensitive and reliable source for inferring homology. I had filtered blast hits based on the above parameters, but the confusion still remain, what percent of coverage (% of length of the gene sequence cove ...
written 3.5 years ago by inayat45shaikh40
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What should be the minimum percent of identity and coverage of blast hits for considering as gene sequence
... Hello group, I had predicted peptide sequences from denovo assembled contigs using abinitio (GENSCAN) approach and subjected it to similarity (BLASTP) search to identify genes in the assemble sequences. But the difficulty i am facing is with minimum percent of identity and coverage of blast hits. W ...
gene alignment sequence blast written 3.6 years ago by inayat45shaikh40 • updated 3.6 years ago by Renesh1.6k
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Answer: A: Genome Annotation Strategies
... Hello group, I have predicted set of genes for large eukaryotic genome from ab initio (GlimmerHMM) and evidence Exonerate & BLASTX based approaches, now i want to make consensus gene sets from both the predictions. initially i was facing issue with gff files loading into mysql database due to p ...
written 4.7 years ago by inayat45shaikh40
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Consensus gene set problem
... Hello group, i have predicted set of genes for large eukaryotic genome from ab initio (GlimmerHMM) and evidence (Exonerate) based approaches, now i want to make consensus gene sets from both the predictions. i am facing issues with GLEAN installation, as its installation manual doesn't provide deta ...
gene written 4.8 years ago by inayat45shaikh40 • updated 4.7 years ago by Biostar ♦♦ 20

Latest awards to inayat45shaikh

Popular Question 3 months ago, created a question with more than 1,000 views. For Somatic and Germline variant calling in ion torrent
Popular Question 5 months ago, created a question with more than 1,000 views. For Somatic and Germline variant calling in ion torrent
Popular Question 22 months ago, created a question with more than 1,000 views. For Somatic and Germline variant calling in ion torrent
Popular Question 22 months ago, created a question with more than 1,000 views. For why Samtools Flagstat Results showing very less reads mapped
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Somatic and Germline variant calling in ion torrent
Popular Question 2.3 years ago, created a question with more than 1,000 views. For why Samtools Flagstat Results showing very less reads mapped
Popular Question 2.8 years ago, created a question with more than 1,000 views. For getting error in runing tblastn
Popular Question 4.7 years ago, created a question with more than 1,000 views. For getting error in runing tblastn

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