User: manjumoorthy95

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Posts by manjumoorthy95

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Comment: C: interpreting local blast output
... thank you for the interpretation ...
written 3 days ago by manjumoorthy950
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interpreting local blast output
... Can anyone tell me how to understand or interpret the result from localblast , in the tab delimited format? I am getting result like this : NODE_1_length_1733100_cov_8.771358 NZ_JMSZ01000042.1 75.07 2230 508 41 85965 88170 275749 273544 0.0 994 NODE_1_length_1733100_cov_8.771358 NZ_JMSZ01 ...
localblast alignment denovo written 4 days ago by manjumoorthy950 • updated 4 days ago by jrj.healey9.7k
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Comment: C: Reads not getting mapped to reference genome
... When using bbmap they do get aligned to the 16s reference but when using bowtie again getting 0 mapping ...
written 4 days ago by manjumoorthy950
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Comment: C: Extracting contaminated reads from the sequenced data
... Thank you, this too worked for me. ...
written 4 days ago by manjumoorthy950
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Comment: C: Extracting contaminated reads from the sequenced data
... Yes thank you , I could seperate reads mapping to each reference genome. But still having one doubt. When I use bowtie or Bowtie2, the paired end reads of my data is not getting mapped to the reference genome, even when the 16s sequence of the reference genome is present in my data. Why could that h ...
written 4 days ago by manjumoorthy950
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Comment: C: Reads not getting mapped to reference genome
... yes I have tried with bowtie2 also but no hits found and also I am using complete reference genomes too. ...
written 4 days ago by manjumoorthy950
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Comment: C: Reads not getting mapped to reference genome
... We are trying to build our own assembly ( de novo assembly) and not 16srRNA sequencing, but whole genome sequencing. And yes the reference genome do contain the 16S RNA sequence. ...
written 5 days ago by manjumoorthy950
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Reads not getting mapped to reference genome
... My sequence data have 3 16srRNA, each belonging to 3 different organism. When I map the paired end reads to the reference genomes of the three organism, using mappers like Bowtie and Bowtie2, it is not showing any hits to the reference genome. Why is it that? ...
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Comment: C: Extracting contaminated reads from the sequenced data
... Thanks a lot. Let me check and let you know. ...
written 5 days ago by manjumoorthy950
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Extracting contaminated reads from the sequenced data
... I have the sequenced data of an organism. but it has three 16srRNA which belong to 3 different organisms. I guess it could be contaminated. How could I extract the contigs belonging to each organism present in the sequence data? ...
genome illumina extraction sequencing written 5 days ago by manjumoorthy950 • updated 5 days ago by genomax60k

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