Moderator: Ido Tamir

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Ido Tamir5.0k
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Location:
Austria
Last seen:
2 hours ago
Joined:
8 years, 4 months 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

<prev • 303 results • page 1 of 31 • next >
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Comment: C: Help with awk command
... Are you sure its the last line and not the first one? Maybe the newline is wrong. Think about what the awk actually does. (edit misread statement). ...
written 11 days ago by Ido Tamir5.0k
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Comment: C: concat fasta sequences based on some common header string
... a good start is going through the biopython tutorial http://biopython.org/DIST/docs/tutorial/Tutorial.html it explains how to read in a fasta file . Although you would maybe also need to understand the basics of python -> split the header , look up the relevant parts in a dictionary etc .. ...
written 4 weeks ago by Ido Tamir5.0k
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Answer: A: More informative GSEA enrichment ggplot
... of course its an R question and not a bioinformatics one and of course your example is not reproducible so thats what you get: something like: + geom_point(aes(shape = sign(NES)) + geom_shape_manual(values = c(24, 1, 25)) ...
written 11 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. Yes, a part of it is driven by CellRanger. ...
written 6 months 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 6 months 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 6 months 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 7 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 7 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 7 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 7 months ago by Ido Tamir5.0k

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