Moderator: Ido Tamir

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Ido Tamir5.0k
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Austria
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Joined:
8 years ago
Email:
i********@imp.ac.at

Tired of missing provenance for your fastq files?

Not knowing which scales the qualities are on?

 

Handling two files for paired end reads instead of one?

 

 

Try bam files instead! A well defined specification (for biological standards). Easy to use tools.

 

Convert illumina basecalls to bam files fresh from the machine: illumina2bam https://github.com/gq1/illumina2bam

 

Posts by Ido Tamir

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Comment: C: BCL files as deliverables from a sequencing center
... Thank you very much for your answer. Yes, a part of it is driven by CellRanger. ...
written 8 weeks ago by Ido Tamir5.0k
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Comment: C: BCL files as deliverables from a sequencing center
... Thank you very much for your answer. We always also offer the complete lane, so they can always demutliplex the data themselves. ...
written 8 weeks ago by Ido Tamir5.0k
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Forum: BCL files as deliverables from a sequencing center
... Hello, recently my customers started to request BCL files from our facility. Is this something sequencing providers or core facilities usually give their customers? Is it a default option or only under some conditions (i.e is there a surcharge in addition to the normal output of FASTQ files)? tha ...
forum serviceprovider corefacility written 8 weeks ago by Ido Tamir5.0k
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Answer: A: Statistics on differentially expressed genes
... Yes its advisable to filter for the reason you have mentioned (i.e. be more sensitive by excluding genes with no chance of being DE or not even being expressed at all in this experiment) and e.g. DESeq2 does this automatically. [Overview Independent filtering of results.][1] [Theory][2] [1]: ht ...
written 3 months ago by Ido Tamir5.0k
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Comment: C: DESeq2-issues with input data
... F2 is the only one that has a low read count compared to the others, but everything else is within a range that the normalisation should handle - and even F2 could be still ok. I don't have any literature reference for this. I guess its rather the high variance between replicates and only 2 replicat ...
written 3 months ago by Ido Tamir5.0k
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Answer: A: How should I handle the raw reads with failed per base sequence content in fastQ
... The adapter starts at the 3' end of your reads, not the 5' (unless its an adapter dimer - i.e. no insert). This is the result of random priming in RNA-Seq. I think [Biases in Illumina transcriptome sequencing caused by random hexamer priming][1] is the first paper on this. This represents real sequ ...
written 3 months ago by Ido Tamir5.0k
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Comment: C: ggplot2 returns empty plot
... all_depth$Chr == "chr6" Chr -> 6 !!! But I guess you also got an error ...
written 3 months ago by Ido Tamir5.0k
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Answer: A: Extract overrepresented sequences from fastq or fastqc
... There are many fastqc report parsers written in different languges. E.g. fastqcr for R: library("magrittr") fastqcr::qc_read(fastqc)$overrepresented_sequences %>% dplyr::mutate(name=paste(">",1:n(),"-",Count,sep=""),fa=paste(name,Sequence,sep="\n")) %>% dply ...
written 4 months ago by Ido Tamir5.0k
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Answer: A: How to take out sequences with barcode?
... You could have been more precise with the difference between your read numbers and the stated numbers. If the stated one is bigger in all samples, then its because often and by default demultiplexing is done with 1 mismatch, which grep can not do. ...
written 4 months ago by Ido Tamir5.0k
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Comment: C: RNA-Seq Differential Expression Bash Scripting Error
... I would recommend for a workflow tool. Unless you are already familiar with bash and its a one off analysis its quickly pays off and its not much more difficult than bash. [tutorial][1] . It can work with modules. [1]: https://www.nextflow.io/example1.html ...
written 6 months ago by Ido Tamir5.0k

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