User: shubhra.bhattacharya

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Posts by shubhra.bhattacharya

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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 8 days ago by shubhra.bhattacharya70
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Comment: C: filter genome above N50 value
... Thanks for your suggestions! ...
written 10 days ago by shubhra.bhattacharya70
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Comment: C: filter genome above N50 value
... Hi! I have two genomes (both draft) of an organism. I have to find out which genome between these two has to be used as a reference for my downstream analysis (transcriptome and SNP profile study etcc) For this genome-genome comparison I have used approaches such as synmap, LAST and mauve but I stil ...
written 10 days ago by shubhra.bhattacharya70
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filter genome above N50 value
... Hi everyone, I want to filter my assembly to get contigs above the N50 value only. How can this be done. --Thanks in advance ...
assembly written 10 days ago by shubhra.bhattacharya70 • updated 10 days ago by Michael Dondrup45k
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Comment: C: Finding out which genes are covered the most
... Hi! Can you help me with understanding no_coverage column means? It would be really great if you tell what the column header mean for each field. I know it's intuitive but it would be helpful. ...
written 16 days ago by shubhra.bhattacharya70
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Comment: C: How to get fasta sequences for CDS if I have proteins IDs?
... Hi! When I try to run the same command, efetch does not take any action but just prints out the help. Any clue why this happens? ...
written 18 days ago by shubhra.bhattacharya70
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dN/dS ratio from .vcf file
... Hi I have 6 .vcf files corresponding to 6 samples. I would like to find dN/dS ratio using these .vcf files but most approaches to this (whatever I could find) were MSA based. Anyone can provide me a way to get this out of my .vcf file. ...
synonmous non-synomous mutation written 21 days ago by shubhra.bhattacharya70
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Comment: C: Finding out which genes are covered the most
... works now! Thanks and I will get back to you in case of doubts. ...
written 21 days ago by shubhra.bhattacharya70
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Comment: C: Finding out which genes are covered the most
... I get the error as below: input: bed file CP019610.1 44 914 B0W97_00010 CP019610.1 991 1309 B0W97_00015 CP019610.1 1365 1695 B0W97_00020 CP019610.1 1691 2060 B0W97_00025 CP019610.1 2165 2465 B0W97_00030 CP019610.1 2571 3099 ...
written 22 days ago by shubhra.bhattacharya70
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Finding out which genes are covered the most
... Hey! I have performed an alignment of my reads (paired end) using Bowtie2. I would like to know which region of the genome is most highly covered. As per my knowledge this can be done using mpileup or Bamcov or visualize the bam file in IGV. But, I want to specifically see which **genes** are th ...
genes coverage written 22 days ago by shubhra.bhattacharya70 • updated 22 days ago by Pierre Lindenbaum115k

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