User: shubhra.bhattacharya
shubhra.bhattacharya • 120
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Posts by shubhra.bhattacharya
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... 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 21 months ago by
shubhra.bhattacharya • 120
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... 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 21 months ago by
shubhra.bhattacharya • 120
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... This can be because there can be gapped alignments occuring or gaps in your sequence. ...
written 22 months ago by
shubhra.bhattacharya • 120
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... awk -F "\t" '{if($3=="tRNA")print}' file.gff > new_file.gff
...
written 22 months ago by
shubhra.bhattacharya • 120
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... We can get fasta from vcf file using vcftools consensus. ...
written 22 months ago by
shubhra.bhattacharya • 120
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... 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 22 months ago by
shubhra.bhattacharya • 120
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... 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 ...
written 22 months ago by
shubhra.bhattacharya • 120
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... Yes,
Use p.aeruginosa as your reference. ...
written 22 months ago by
shubhra.bhattacharya • 120
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... 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 22 months ago by
shubhra.bhattacharya • 120
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... Hey!
How do I get to print the co-ordinates of the match? ...
written 22 months ago by
shubhra.bhattacharya • 120
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19 months ago,
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For Filter all the common SNP's in different vcf files(corresponding to different samples)
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For A: Can gffread extract specific region sequences from vcf or fasta file?
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