User: shubhra.bhattacharya

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Posts by shubhra.bhattacharya

<prev • 67 results • page 1 of 7 • next >
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Comment: C: assembly of contigs into scaffolds
... Usually reads will have adapter sequences in them which may be removed prior to assembly (Tools like cutadapt etc are available for the same). https://bioinformatics.uconn.edu/bacterial-genome-assembly-tutorial/ for more info on different assemblers. Meanwhile many tutorials for WGS assembly is ...
written 5 months ago by shubhra.bhattacharya120
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Answer: A: assembly of contigs into scaffolds
... Hi! Few questions first: 1)What do you mean when you say "assembled into reads". 2)Also what reads are these (Long reads,short reads etc?) 3)Are you processing your reads in any way? I have done fungal assembly of 150X2 reads (150 bases,Paired end) using SPAdes and I got satisfactory results. ...
written 5 months ago by shubhra.bhattacharya120
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Answer: A: How come Alignment length is longer than Subject sequence length?
... This can be because there can be gapped alignments occuring or gaps in your sequence. ...
written 5 months ago by shubhra.bhattacharya120
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Comment: C: Can gffread extract specific region sequences from vcf or fasta file?
... awk -F "\t" '{if($3=="tRNA")print}' file.gff > new_file.gff ...
written 5 months ago by shubhra.bhattacharya120
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Comment: C: Can gffread extract specific region sequences from vcf or fasta file?
... We can get fasta from vcf file using vcftools consensus. ...
written 5 months ago by shubhra.bhattacharya120
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Answer: A: Can gffread extract specific region sequences from vcf or fasta file?
... I am not sure about gffread but extracting specific gene or all genes etc can be done using bedtools. https://bedtools.readthedocs.io/en/latest/content/tools/getfasta.html ...
written 5 months ago by shubhra.bhattacharya120
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Plasmid obtained from assembly is incomplete.
... Hi! The sample I am using for analysis is plasmid DNA. I performed assembly of the reads using SPAdes and plasmid identification using Recycler. However the plasmid being identified is 1000 bases in size whereas the original construct is 5000 bases in size. What can be the reason for it? Also, how ...
plasmid recycler assembly written 5 months ago by shubhra.bhattacharya120
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Comment: C: How can I extract SNP from bacterial genome?
... Yes, Use p.aeruginosa as your reference. ...
written 5 months ago by shubhra.bhattacharya120
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Answer: A: How can I extract SNP from bacterial genome?
... The question is very broad. It does not give an idea about the objective of snp calling etc. Many online tutorials/papers etc are present in exhaustive fashion about the same. You can read this for starters though: https://www.ebi.ac.uk/sites/ebi.ac.uk/files/content.ebi.ac.uk/materials/2014/140217_ ...
written 5 months ago by shubhra.bhattacharya120
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Comment: C: Regular expression matching with Python and biopython SeqIO
... Hey! How do I get to print the co-ordinates of the match? ...
written 6 months ago by shubhra.bhattacharya120

Latest awards to shubhra.bhattacharya

Supporter 5 months ago, voted at least 25 times.
Scholar 5 months ago, created an answer that has been accepted. For A: Can gffread extract specific region sequences from vcf or fasta file?

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