User: tonja.r

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tonja.r430
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UK
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Posts by tonja.r

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Forum: Is it possible to change a username?
... Hello, due to some private reasons, I need to change my username on Biostars. Is it possible? ...
forum written 19 months ago by tonja.r430 • updated 19 months ago by Pierre Lindenbaum108k
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Comment: C: demultiplexing with fastq having barcode and primer sequence
... Cand I just search for the half of the barcode in the reads, for instance? It is my original dataset already. ...
written 20 months ago by tonja.r430
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Comment: C: demultiplexing with fastq having barcode and primer sequence
... I am having an issue because when the adapter was cut away, it could have happened that some first bases of the barcode were cut out as well ...
written 20 months ago by tonja.r430
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Comment: C: demultiplexing with fastq having barcode and primer sequence
... yes, exactly, I corrected it ...
written 20 months ago by tonja.r430
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Comment: C: demultiplexing with fastq having barcode and primer sequence
... I was told that they used primer for PCR, then they hanged the barcodes and adapters and sequenced it. What I find my reads is that the barcode comes before the primer, so it corresponds exactly to what I was told. ...
written 20 months ago by tonja.r430
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demultiplexing with fastq having barcode and primer sequence
... I have paired-end Illumina reads with barcode and primer sequence. Barcode and primer sequence are just in .txt file. The experiment was following: Primer was used for PCR and then they hanged the experiment tag (barcode) and the adapter. So, the read are following: > barcode_sequence-PCR_primer ...
next-gen demultiplex sequencing written 20 months ago by tonja.r430
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demultiplexing with fastq but without barcode read fastq
... It seems that I am missing something, so I will just describe my problem. I have paired-end illumina reads in fastq format. In .txt I have the sequence for forward and reverse primers and tags for each experiment. I will attach an example file. The read has following format: tag-primer-fragment I ne ...
next-gen sequencing written 20 months ago by tonja.r430 • updated 20 months ago by charbo2440
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Comment: C: single end reads, reverse and forward primer
... I thought that in single end we sequence only from one end, say P7, whereas P5 is attached to the flow cell. Also, after amplification the reverse reads are washed away, meaning we have only forward reads. So, there is always only one primer for each sequence. ...
written 20 months ago by tonja.r430
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single end reads, reverse and forward primer
... I have forward and reverse single end reads. I can distinguish them from fastq file according to a forward or a reversed primer. However, I do not understand how one can get reversed and forward single end reads from the sequencing. If I look at the forward reads in FastQC, the per-base quality lo ...
next-gen written 20 months ago by tonja.r430 • updated 20 months ago by dariober9.2k
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Comment: C: RSeQC infer_experiment.py results interpretation for cuffdiff and featureCounts
... So, I did ask, how did you understand it from the results? ...
written 22 months ago by tonja.r430

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