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I want to download the original BAM files that the authors had uploaded to SRA. Normally, I would just use sam-dump, but the files are having issues that seem related...
Asked on 12/06/2020
1 answerfirst time I post here so, please, be patient.So I am currently working with Entrez (Biopython) in order to retrieve the number of articles for a given disease/indication. My...
Asked on 12/05/2020 by Nutarelli Federico
0 answerI have several groups of 16S rRNA sequences associated with taxonomic groups (let's call them A, B and C). The sequences within each group have a common ancestor and are...
Asked on 12/05/2020
1 answerIf continuous-time Markov models contain a parameter q that denotes the instantaneous rate of change and a global/strict clock model is the overall rate of evolution, how are these two...
Asked on 12/04/2020
1 answerI am trying to reproduce the work of this paper[1], and I have run StringTie successfully, but after that I have to run...
Asked on 12/03/2020 by fatima
1 answerSnakemake is not really designed to store temporary files to local disk, but in the documentation, they suggest a workaround using "shadow rules". The problem I have...
Asked on 12/02/2020 by Kamil S Jaron
1 answerfrom Bio import SeqIOfrom Bio import Alignref_seq_1 = SeqIO.read('C:/Users/King_Arthur/Desktop/ref_seq/segment 1/ref_seq_8.fasta','fasta')seq1 = SeqIO.read('C:/Users/King_Arthur/Desktop/file/segment 1/Myfile_1 (1).fasta','fasta')aligner = Align.PairwiseAligner()aligner.mode = 'global'aligner.match_score = 1aligner.mismatch_score = -2aligner.gap_score = -2alignments = aligner.score(ref_seq_1.seq , seq1.seq)print(alignments)for alignment...
Asked on 12/01/2020 by Neeleshwar Pandey
1 answerI have a couple of hundred bacterial sequences of 2-30 genes of interest each, recovered from metagenomics. None of them encode rRNA. Normally I'd just BLAST the one gene I...
Asked on 12/01/2020
2 answerIs there any user friendly way to find rare mutations in the individual human whole genome sequencing raw data? (from Dante, 30x coverage). To be more specific, I want to...
Asked on 11/29/2020 by musinn
1 answerI have several matrix from computematrix of deeptools. I need to merge two of them using "computeMatrixOperations cbind -m input1.mat.gz input2.mat.gz -o output.mat.gz"but I am running to error "/computeMatrixOperations.py",...
Asked on 11/28/2020
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