User: jorja

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jorja0
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Posts by jorja

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Comment: C: Sorting fq data into groups with missing barcode info?
... These are the data I got and that basically this is it... My guess is like your guess that they are two ends, but does not seems so... Let me search the sequence coordinate and compare the of the merged one vs raw read and report to you! ...
written 8 weeks ago by jorja0
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Comment: C: Sorting fq data into groups with missing barcode info?
... Super! That is very nice to know. Thank you, Albert! I will do it this way then! ...
written 8 weeks ago by jorja0
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Comment: C: Sorting fq data into groups with missing barcode info?
... Thank you, Albert! Glad to find someone suggesting the same thing I tried too! But things might not be that easy... Because what I got by this method does not match the QC report they gave us (the read numbers). Makes me wonder what I did was wrong... ...
written 8 weeks ago by jorja0
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Comment: C: Sorting fq data into groups with missing barcode info?
... Hi genomax, I believe you mean using deML right? Based on reading the document of the deML, I believe it using a method that is not a simple location matching, right? It suggested maximum likelihood method that is similar to sequence mapping? I believe you have the right point, (and this answer ...
written 8 weeks ago by jorja0
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Comment: C: Sorting fq data into groups with missing barcode info?
... I just did! And I put the first read of every file that I can find in the folder. Hope that helps. And also I put the QC file they generated for us too. ...
written 8 weeks ago by jorja0
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Comment: C: Sorting fq data into groups with missing barcode info?
... Thank you, swbarnes2! So I was only given this pile of data without knowing what the sequencing service did... Assume what you said is true (non-standard library preps that might put the sample barcode in read 2 instead of the usual index position), how should I proceed? ...
written 8 weeks ago by jorja0
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Comment: C: Sorting fq data into groups with missing barcode info?
... Thank you, genomax! I agree centroid info seems not important. Put it here just in case... Nice to confirm. Your link is very useful. Apparently, it means I cannot simply separate files based on their header... I will try the package in the link! ...
written 9 weeks ago by jorja0
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Comment: C: Sorting fq data into groups with missing barcode info?
... What do you me by non-standard? This is my first time saw this kind of files, so not much to compare with.... ...
written 9 weeks ago by jorja0
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Comment: C: Sorting fq data into groups with missing barcode info?
... These are regular Illumina barcodes. We are running this by ourselves because we cannot reach the provider any more... So I am basically on my own. When you said that the barcode and reads do not match, do you mean their header line does not match? This is my bad. I did not paste the matching one ...
written 9 weeks ago by jorja0
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Comment: A: Sorting fq data into groups with missing barcode info?
... I am very sad to see that there are 89 views and no answer yet... Can someone maybe point to me how I can improve my post to make it clearer to the readers? Or what additional info I need to put in? Thanks! ...
written 9 weeks ago by jorja0

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