Moderator: Ido Tamir

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Ido Tamir5.1k
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Location:
Austria
Last seen:
9 hours ago
Joined:
9 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

<prev • 320 results • page 1 of 32 • next >
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Answer: A: RNA-Seq differential gene expression without biological and technical replicates
... https://www.biostars.org/p/398152/ maybe look at NOI-Seq http://seqanswers.com/forums/showpost.php?p=107433&postcount=2 or just do it in excel: sort by ratio from high to low, same reliability (but no normalisation). The result is not to be trusted. It would have been better to use just 1 deve ...
written 20 days ago by Ido Tamir5.1k
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Answer: C: How to get DE genes without replicates using EdgeR
... in the 2. part you called differential expression on a matrix without gene names as row names filled with random numbers ...
written 20 days ago by Ido Tamir5.1k
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Comment: C: How many of the reads end up being counted by HTSeq count
... better to sum up without the extra lines, sum up with the extra lines and then divide. ...
written 5 weeks ago by Ido Tamir5.1k
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Answer: A: How many of the reads end up being counted by HTSeq count
... https://htseq.readthedocs.io/en/master/count.html#usage at the bottom of the file you have some lines with some special counters you have to exclude for calculating the ratio. All of it has to sum up to the number of input reads. http://bioinf.wehi.edu.au/featureCounts/ is faster and gives you the s ...
written 5 weeks ago by Ido Tamir5.1k
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Comment: C: D' and r2 graphics in R
... you already asked a similar question 11 days ago here: https://www.biostars.org/p/442374/ The reason why nobody answered this question is that its written without any effort on making it understandable, but you want effort in the answer: https://www.biostars.org/p/75548/ ...
written 6 weeks ago by Ido Tamir5.1k
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Comment: C: How can I extract the sequencing reads containing a specific linker/tag?
... please upvote useful answers and accept one as the best, not thank in a comment ...
written 8 weeks ago by Ido Tamir5.1k
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Answer: A: How can I extract the sequencing reads containing a specific linker/tag?
... you can use cutadapt for this serching for the linker allowing the appropriate number of mutations action = none and saving the reads with/without linker into separate files ...
written 9 weeks ago by Ido Tamir5.1k
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Answer: A: Adding annotations to the bam file from the txt file
... "best" is subjective. In python I would read in the the annotations per name into a dict, then iterate through the bam file with pysam adding the annotation based on the read name writing each one out into a new bam file ...
written 9 weeks ago by Ido Tamir5.1k
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Comment: C: problem installing cutadapt
... sorry, did not read, but that is very wierd. Did you use a new conda environment? did you activate the new environment? look at $PATH, $PYTHONPATH , `which cutadapt` if there are discrepancies that would explain the problem. i.e. which version does get picked up ...
written 5 months ago by Ido Tamir5.1k
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Comment: A: problem installing cutadapt
... start using conda, it helps a bit: https://bioconda.github.io/user/install.html#install-conda ...
written 5 months ago by Ido Tamir5.1k

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Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Shall We Go Back To Stackexchange?
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