User: zach

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zach0
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Posts by zach

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Comment: C: Barcode Fastq Header - Adding Characters
... deML does not seem to work with my data for some reason. It seems that I should still attempt to add the index sequence to the header of each sample, within the barcode file. ...
written 3 months ago by zach0
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Comment: C: Barcode Fastq Header - Adding Characters
... Thanks. I have looked at the post you linked and have tried using deML. I ran into several errors and am currently discussing with the developer about this ...
written 3 months ago by zach0
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Comment: C: Barcode Fastq Header - Adding Characters
... All the samples are in R1. The same is for R2, and I1 as well. ...
written 3 months ago by zach0
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Comment: C: Barcode Fastq Header - Adding Characters
... The sequence index in the header for all the other samples are different, eg: @DGZN8DQ1:549:H7C23BCXX:2:1101:1087:1870 1:N:0:CGTCGTATGAAT vs @DGZN8DQ1:549:H7C23BCXX:2:1101:1126:1870 1:N:0:TTTGCATCAGGG vs @DGZN8DQ1:549:H7C23BCXX:2:1101:1189:1870 1:N:0:CCGTCTATGTTT and so on corresponding to t ...
written 3 months ago by zach0
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Comment: C: Barcode Fastq Header - Adding Characters
... Hi all. Thank you so much for the commands and quick help - I used 'awk' and it worked to make the barcode header lines: @DGZN8DQ1:549:H7C23BCXX:2:1101:1087:1870 1:N:0 However, when demux-ing, I received another error message for mismatched seq description: N:0, N:0:CGTCGTATGAAT, and N:0:CGTCGTATGA ...
written 3 months ago by zach0
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Barcode Fastq Header - Adding Characters
... I'm new with Linux and would appreciate any help with this. My forward fastq file has this type of header line for each sample: @DGZN8DQ1:549:H7C23BCXX:2:1101:1087:1870 1:N:0:CGTCGTATGAAT But my barcode fastq file only has: @DGZN8DQ1:549:H7C23BCXX:2:1101:1087:1870 This is not allowing me to demu ...
sequencing written 3 months ago by zach0
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Comment: C: Qiime2 Demux Error
... Regarding my 2nd question, is there a way I could add the sequence of the index (from forward sequence file) to the barcode file headers for each sample? I am quite new to the Linux system. I am wondering how I could possibly utilise the 'paste' command (?) to solve this problem? I would be gratef ...
written 3 months ago by zach0
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Comment: C: Qiime2 Demux Error
... Thanks for all the answers, genomax. From the link you provided, I am trying to demux with deML as it seems like a promising solution. If I successfully get the output in fastq format, is there a way to convert the demux-ed document to .qza format? I need it in .qza for Qiime2 donwstream analyses. ...
written 3 months ago by zach0
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Comment: A: Qiime2 Demux Error
... I also noticed another potential and more likely problem. The sequence header is this: @DGZN8DQ1:549:H7C23BCXX:2:1101:1087:1870 1:N:0:CGTCGTATGAAT Whereas the barcode header is this: @DGZN8DQ1:549:H7C23BCXX:2:1101:1087:1870 I think the error is probably because the barcode header lines d ...
written 3 months ago by zach0 • updated 3 months ago by genomax80k
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Qiime2 Demux Error
... Hello there, I hope there is someone experienced in Qiime2 who could help me please. I am demultiplexing sequence data with the command below: qiime demux emp-paired –m-barcodes-file 54386_mapping_file.txt –m-barcodes-column BarcodeSequence –p-rev-comp-mapping-barcodes –i-seqs emp-paired-e ...
qiime2 demux written 3 months ago by zach0 • updated 3 months ago by genomax80k

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