User: deepthithomaskannan

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Canada
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Posts by deepthithomaskannan

<prev • 64 results • page 1 of 7 • next >
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Comment: C: Picard Exception: Illegal Mate State
... Try bedtools bamtofastq. Also check this link http://seqanswers.com/forums/showthread.php?t=40117 Deeps ...
written 23 months ago by deepthithomaskannan150
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Kraken output to Krona Tools: What can be selected as magnitude
... Hi all, I am trying to use Kraken (http://ccb.jhu.edu/software/kraken/) output file as an input to KronaTools (metagenomic visualization tool)script ktImportTaxonomy.  Basically I am doing the taxonomy classification using Kraken and trying to visualize it using Krona tools.  I would like to know w ...
krona magnitude kraken written 23 months ago by deepthithomaskannan150
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Comment: C: MEGAN and Kraken for taxonomy classification
... Thank you Phil.  Deepthi ...
written 23 months ago by deepthithomaskannan150
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(Closed) Tool for plotting Kraken output
... Hi, I am trying to do taxonomy classification for my reads. I tried Kraken software. Is there any tools available for plotting Kraken output? Thanks, Deepthi ...
kraken output plot written 23 months ago by deepthithomaskannan150
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MEGAN and Kraken for taxonomy classification
... Hi, I am trying to do taxonomy classification for my unmapped (to reference genome) reads. I tried both Megan (http://ab.inf.uni-tuebingen.de/software/megan5/ ) and kraken(http://ccb.jhu.edu/software/kraken/ ). In kraken I can use read files directly as the input, whereas in Megan I have to make t ...
taxonomy kraken readfile megan written 23 months ago by deepthithomaskannan150 • updated 20 months ago by ramanandan.prabhakaran20
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(Closed) MEGAN or Karaken
... Hi, I would like to do taxonomy classification on my data.  How can I compare MEGAN and Kraken tools?  I tried both of them.  But no idea how to compare the results.  Thanks, Deepthi   ...
kraken megan written 23 months ago by deepthithomaskannan150
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Comment: C: How to calculate organism relative abundance from Illumina metagenomic data?
... Hi, I am also doing same kind of analysis.  What do you mean by "different samples may have different sequencing levels" ? Thanks, D     ...
written 24 months ago by deepthithomaskannan150
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Comment: C: Convert Solid Xsq To Fastq Without Intermediates Files
... Hi William, I am getting errors while I am trying to install your XSQConverter tool.  I asked about it in the issue section of GitHub repository(https://github.com/WimS83/XSQConverter/issues).  Could please have a look at it. Jan 13: Hi William, I updated the issue in github.  Could you please che ...
written 2.0 years ago by deepthithomaskannan150
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samtools flagstat interpretation- total value
... Hi all, I got the flagstat output for my bam file as follows: 1639094206 + 0 in total (QC-passed reads + QC-failed reads) 0 + 0 duplicates 1213460872 + 0 mapped (74.03%:-nan%) 1639094206 + 0 paired in sequencing 819547103 + 0 read1 819547103 + 0 read2 376403646 + 0 properly paired (22.96%:-nan%) 7 ...
flagstat samtools total written 2.3 years ago by deepthithomaskannan150 • updated 2.3 years ago by Pierre Lindenbaum88k
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Comment: C: Unaligned Reads From Bowtie2
... I assume the --un option will give you the 67801 reads which are unaligned. ...
written 2.4 years ago by deepthithomaskannan150

Latest awards to deepthithomaskannan

Popular Question 2.3 years ago, created a question with more than 1,000 views. For What Is A Better Choice For Clustering Illumina Sequences Cd-Hit Or Uclust?
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Remove Duplicate Reads From Fasta File
Popular Question 2.5 years ago, created a question with more than 1,000 views. For What Is A Better Choice For Clustering Illumina Sequences Cd-Hit Or Uclust?
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Sequence Length Distribution From A Fastq File
Supporter 2.5 years ago, voted at least 25 times.
Popular Question 2.8 years ago, created a question with more than 1,000 views. For Sequence Length Distribution From A Fastq File
Popular Question 4.0 years ago, created a question with more than 1,000 views. For Trimming Adapters For Paired-End Sequences
Popular Question 4.4 years ago, created a question with more than 1,000 views. For How To Interpret The Flag Field In The Sam Specification

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