User: jeccy.J

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jeccy.J50
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Posts by jeccy.J

<prev • 62 results • page 1 of 7 • next >
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Rarefaction curve of Shotgun metagenome
... We have done a large scale shotgun metagenome over 100 samples and analysed using metaphlan2. Can anybody help me out how to perform a Rarefaction analysis of metaphal2 output, as i can did not see anything motioned about Rarefaction on metaphaln web page. In case of amplicon we can subsample the re ...
sequence metagenome written 9 days ago by jeccy.J50
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Comment: C: Pangenome Analysis using Roary tool
... Could you please explain how to extract the SNPs from the final output of Roary. ...
written 4 months ago by jeccy.J50
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Comment: C: Error while importing data into Qiime2
... The file name are as below : Fan1_S26_L001_R1_001.fastq Fan7_S34_L001_R1_001.fastq Fan1_S26_L001_R2_001.fastq Fan7_S34_L001_R2_001.fastq Fan4_S31_L001_R1_001.fastq Fan9_S36_L001_R1_001.fastq Fan4_S31_L001_R2_001.fastq Fan9_S36_L001_R2_001.fastq head of one file @M02975:138:000000000-CFCFY:1 ...
written 4 months ago by jeccy.J50
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Error while importing data into Qiime2
... Hi everyone, I am trying to import fastq files (16s amplicon sequence data) into qiime2 pipeline but some error occurred. Can anyone please help me out to solve the error. $ qiime tools import --type SampleData[PairedEndSequencesWithQuality] --input-path primer_trimmed_fastqs --output-path r ...
sequence written 4 months ago by jeccy.J50 • updated 4 months ago by swbarnes27.0k
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How to do alpha and beta diversity with shougun metagenome data
... Hi Everyone, Can anyone suggest me any tools or R package for shotgun metagenome alpha and beta diversity analysis. Currently i am using kaiju for classification of all the raw reads. I have a final csv file with the taxa abundance (number of total reads) of each sample. For example : ...
metagenom shotgun written 8 months ago by jeccy.J50 • updated 6 months ago by gb1.2k
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Comment: C: How to remove contamination reads from fastq flle
... @genomax i tried as per your suggestion but could not make any improvement in reads for the negative control. Do you have any other suggestion/idea? ...
written 8 months ago by jeccy.J50
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Comment: C: How to remove contamination reads from fastq flle
... No i did not try yet. I will have a try. My guess was the reads which is coming from negative control(mainly from kit and reagents) that must be present in positive control as well. So if I remove particular those reads and the remaining will be from positive control. But i am not sure that i am ri ...
written 8 months ago by jeccy.J50
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Comment: C: How to remove contamination reads from fastq flle
... Thanks for your reply. Repeating the experiment is not possible as the patients samples not easy to obtain. I agreed with you that if the contaminant reads and true signal reads are exactly similar then there is high chance to lose the reads. But let's say contaminant and true signal have same spec ...
written 8 months ago by jeccy.J50
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Comment: C: How to remove contamination reads from fastq flle
... For species point of view it will not change I think. I have shotgun metagenome data and i am removing only lab reagents contamination reads so do you think could it be a problem? Moreover, i rarely saw people hardly care about those reads but from my point of view one should consider those reads c ...
written 8 months ago by jeccy.J50
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Comment: C: How to remove contamination reads from fastq flle
... yes, i have merged those positive control reads by using : $ cat R1.fastq R2.fastq > merge_R1_R2.fastq and i have merged all negative control reads also in similar way. Could you please let me know what should be my next step? How can i mapped those one against other? ...
written 8 months ago by jeccy.J50

Latest awards to jeccy.J

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