User: biobudhan

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biobudhan20
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India
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2 years, 2 months ago
Joined:
5 years, 5 months ago
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Posts by biobudhan

<prev • 8 results • page 1 of 1 • next >
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Is GATK overestimating the heterozygous calls?
... I have 24 genotypes distributed in 4 different populations. I used HaplotypeCaller with the option –ERC –GVCF and obtained the vcf file for each genotype. Then combined all the genotypes to a single vcf file with GenotypeGVCFs option. Is there a way to tell GATK to label a variant site as „Heteroz ...
vcf gatk heterozygous snp written 2.2 years ago by biobudhan20 • updated 2.2 years ago by andrew.j.skelton735.8k
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pairwise alignment for multiple sequences in a file
... I have about 10 protein/DNA sequences in a file in FASTA format and would like to do a pairwise alignment for all possible combinations in this file. Example: Seq1 vs Seq2 Seq1 vs Seq3 Seq1 vs Seq4 and so on. Are there tools that can perform this? ...
pairwise fasta alignment written 2.7 years ago by biobudhan20 • updated 2.7 years ago by st.ph.n2.5k
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Comment: C: Sequence alignment length
... Thank you. :-) I will check this option! ...
written 2.7 years ago by biobudhan20
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Comment: C: Sequence alignment length
... I am sorry for the confusion. I tried to differentiate the ID from the sequences using the bold and italic option on biostars. To answer your questions: What format is this? : All my files are in .aln format (alignment format of clustal) Do all the alignments include two stars in the 5' and 3'-end ...
written 2.7 years ago by biobudhan20
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Sequence alignment length
... I have a folder with over 1000 alignments performed using MAFFT. Are there any tools that can tell the length of the sequence alignment? example: *seq1* **ATGC-CTGA-TTTGGG-** *seq2* **ATGCCCTGATTTT-GGC** In this case the alignment length is: 17 ...
length multiple sequence alignment written 2.7 years ago by biobudhan20
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Fastsimcoal for transcriptome data
... Hello, Is it possible/ good idea to use fastsimcoal to infer demography using transcriptome data ? ...
demography fastsimcoal written 3.1 years ago by biobudhan20 • updated 2.9 years ago by Biostar ♦♦ 20
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adegent for Tajima's D:
... Hello everyone, I am trying to use adegent in R for calculating the Tajima's D. I have a DNA.bin object containing my sequences from different populations. The sequences are of varying length because of the SNP and indels in them. I get the following error when I run the tajima.test function:  Err ...
tajima fasta snp adegent written 4.0 years ago by biobudhan20 • updated 4.0 years ago by Brice Sarver3.1k
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Comment: C: Qst Values calculation
... thanks very much, i will check that out!!   ...
written 4.6 years ago by biobudhan20

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Popular Question 2.7 years ago, created a question with more than 1,000 views. For Qst Values calculation

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