User: shubhra.bhattacharya

Reputation:
120
Status:
Trusted
Location:
Last seen:
20 hours ago
Joined:
1 year, 1 month ago
Email:
s*******************@genotypic.co.in

Posts by shubhra.bhattacharya

<prev • 67 results • page 1 of 7 • next >
0
votes
1
answer
154
views
1
answers
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 6 weeks ago by shubhra.bhattacharya120
1
vote
1
answer
154
views
1
answers
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 6 weeks ago by shubhra.bhattacharya120
1
vote
2
answers
170
views
2
answers
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 7 weeks ago by shubhra.bhattacharya120
1
vote
1
answer
156
views
1
answers
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 7 weeks ago by shubhra.bhattacharya120
1
vote
1
answer
156
views
1
answers
Comment: C: Can gffread extract specific region sequences from vcf or fasta file?
... We can get fasta from vcf file using vcftools consensus. ...
written 7 weeks ago by shubhra.bhattacharya120
1
vote
1
answer
156
views
1
answers
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 7 weeks ago by shubhra.bhattacharya120
0
votes
0
answers
141
views
0
answers
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 7 weeks ago by shubhra.bhattacharya120
0
votes
1
answer
176
views
1
answers
Comment: C: How can I extract SNP from bacterial genome?
... Yes, Use p.aeruginosa as your reference. ...
written 7 weeks ago by shubhra.bhattacharya120
0
votes
1
answer
176
views
1
answers
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 7 weeks ago by shubhra.bhattacharya120
0
votes
1
answer
4.4k
views
1
answers
Comment: C: Regular expression matching with Python and biopython SeqIO
... Hey! How do I get to print the co-ordinates of the match? ...
written 10 weeks ago by shubhra.bhattacharya120

Latest awards to shubhra.bhattacharya

Supporter 7 weeks ago, voted at least 25 times.
Scholar 7 weeks ago, created an answer that has been accepted. For A: Can gffread extract specific region sequences from vcf or fasta file?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 789 users visited in the last hour