Moderator: Ido Tamir

gravatar for Ido Tamir
Ido Tamir5.1k
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Austria
Last seen:
17 minutes ago
Joined:
9 years, 8 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 • 328 results • page 2 of 33 • next >
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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 8 months 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 8 months 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 8 months 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 9 months 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 months 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 months 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 13 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 13 months ago by Ido Tamir5.1k
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Comment: C: HTseq does not generate any counts file
... https://docs.conda.io/projects/conda/en/latest/user-guide/getting-started.html ...
written 13 months ago by Ido Tamir5.1k
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Comment: C: HTseq does not generate any counts file
... I guess you use a different python than HTseq count. Best and easiest is you switch to conda and create your own environment independent of the administrators. ...
written 13 months ago by Ido Tamir5.1k

Latest awards to Ido Tamir

Popular Question 8 weeks ago, created a question with more than 1,000 views. For Duplication And Quality Control In Published Ngs Data
Scholar 3 months ago, created an answer that has been accepted. For A: R multiple parameters
Good Answer 11 months ago, created an answer that was upvoted at least 5 times. For A: Illumina Read Names: /2 Vs. /3
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Shall We Go Back To Stackexchange?
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: Shall We Go Back To Stackexchange?
Scholar 23 months ago, created an answer that has been accepted. For A: Overlaid XY plot with two different colors for control and target genes
Commentator 23 months ago, created a comment with at least 3 up-votes. For C: Picking A Programming Language And Where To Begin
Teacher 2.6 years ago, created an answer with at least 3 up-votes. For A: Shall We Go Back To Stackexchange?
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Teacher 3.3 years ago, created an answer with at least 3 up-votes. For A: Shall We Go Back To Stackexchange?
Popular Question 3.4 years ago, created a question with more than 1,000 views. For Duplication And Quality Control In Published Ngs Data
Appreciated 3.4 years ago, created a post with more than 5 votes. For A: Shall We Go Back To Stackexchange?
Appreciated 3.4 years ago, created a post with more than 5 votes. For A: Shall We Go Back To Stackexchange?
Scholar 3.6 years ago, created an answer that has been accepted. For A: Overlaid XY plot with two different colors for control and target genes
Teacher 3.9 years ago, created an answer with at least 3 up-votes. For A: Shall We Go Back To Stackexchange?
Teacher 3.9 years ago, created an answer with at least 3 up-votes. For A: Shall We Go Back To Stackexchange?
Scholar 3.9 years ago, created an answer that has been accepted. For A: Overlaid XY plot with two different colors for control and target genes
Good Answer 4.3 years ago, created an answer that was upvoted at least 5 times. For A: Illumina Read Names: /2 Vs. /3
Appreciated 4.4 years ago, created a post with more than 5 votes. For A: Shall We Go Back To Stackexchange?
Good Answer 4.4 years ago, created an answer that was upvoted at least 5 times. For A: Illumina Read Names: /2 Vs. /3
Popular Question 4.7 years ago, created a question with more than 1,000 views. For Duplication And Quality Control In Published Ngs Data
Commentator 4.7 years ago, created a comment with at least 3 up-votes. For C: Picking A Programming Language And Where To Begin
Good Answer 5.0 years ago, created an answer that was upvoted at least 5 times. For A: Illumina Read Names: /2 Vs. /3
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