Moderator: Ido Tamir

gravatar for Ido Tamir
Ido Tamir5.1k
Reputation:
5,140
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Location:
Austria
Last seen:
13 minutes ago
Joined:
9 years, 3 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 • 327 results • page 1 of 33 • next >
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Comment: C: Data management in R, perl or python
... they want the suffix after the 2 letters collected and appended. This is a basic programming question for which they should show at least some effort in some language ...
written 15 days ago by Ido Tamir5.1k
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Answer: A: New data transformation tool for Windows and Mac
... This looks a lot like simplified knime https://www.knime.com/ which has an open source gui besides commercial offerings ...
written 6 weeks ago by Ido Tamir5.1k
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Comment: C: how to get total read count, mapped read count and unmapped read count from mult
... you are asking two questions: a) how to loop over files b) how to extract mapped counts. a) is not really a topic for this site and you can find answers on stackoverflow or google. b) was answered multiple times. ...
written 6 weeks ago by Ido Tamir5.1k
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Comment: C: RNA-Seq and no of reads
... https://hbctraining.github.io/Intro-to-rnaseq-hpc-O2/lessons/03_alignment.html ...
written 7 weeks ago by Ido Tamir5.1k
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Comment: C: Running a code in batch mode on a list of files
... you seem to be wrinting everything into out. im not good with bashs quoting rules, so to be safe: for i in $(find ..); do awk 'cmd' $f > ${f}_out.txt ; done This is a rather complicated statement and you should create a script from it that you can (re)use in a loop and reuse it. Saves time i ...
written 9 weeks ago by Ido Tamir5.1k
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Comment: C: Extracting rows on basis of specific column values in R
... please work through any of the many online R tutorials. You could also look up "how to ask questions" and unfortunately it looks like a correct tagging of posts tutorial is also necessary. Maybe you think the $ would signify a regex end matching? try endsWith ...
written 9 weeks ago by Ido Tamir5.1k
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Comment: C: Trouble with choosing the right reference transcriptome file for mm10
... the ncrna in the name could already give you a hint what the file represents - so I would change the file you use. But this is completely independent of the question why you think that two different programs should deliver identical results for a complex task implemented with different assumptions ...
written 11 weeks ago by Ido Tamir5.1k
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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 3 months 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 3 months 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 3 months ago by Ido Tamir5.1k

Latest awards to Ido Tamir

Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Shall We Go Back To Stackexchange?
Good Answer 7 months ago, created an answer that was upvoted at least 5 times. For A: Illumina Read Names: /2 Vs. /3
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Shall We Go Back To Stackexchange?
Scholar 19 months ago, created an answer that has been accepted. For A: Overlaid XY plot with two different colors for control and target genes
Commentator 19 months ago, created a comment with at least 3 up-votes. For C: Picking A Programming Language And Where To Begin
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: Shall We Go Back To Stackexchange?
Teacher 2.6 years ago, created an answer with at least 3 up-votes. For A: Shall We Go Back To Stackexchange?
Teacher 2.9 years ago, created an answer with at least 3 up-votes. For A: Shall We Go Back To Stackexchange?
Popular Question 3.0 years ago, created a question with more than 1,000 views. For Duplication And Quality Control In Published Ngs Data
Appreciated 3.0 years ago, created a post with more than 5 votes. For A: Shall We Go Back To Stackexchange?
Appreciated 3.1 years ago, created a post with more than 5 votes. For A: Shall We Go Back To Stackexchange?
Scholar 3.2 years ago, created an answer that has been accepted. For A: Overlaid XY plot with two different colors for control and target genes
Teacher 3.5 years ago, created an answer with at least 3 up-votes. For A: Shall We Go Back To Stackexchange?
Teacher 3.5 years ago, created an answer with at least 3 up-votes. For A: Shall We Go Back To Stackexchange?
Scholar 3.5 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 3.9 years ago, created an answer that was upvoted at least 5 times. For A: Illumina Read Names: /2 Vs. /3
Appreciated 4.0 years ago, created a post with more than 5 votes. For A: Shall We Go Back To Stackexchange?
Good Answer 4.0 years ago, created an answer that was upvoted at least 5 times. For A: Illumina Read Names: /2 Vs. /3
Popular Question 4.3 years ago, created a question with more than 1,000 views. For Duplication And Quality Control In Published Ngs Data
Commentator 4.4 years ago, created a comment with at least 3 up-votes. For C: Picking A Programming Language And Where To Begin
Good Answer 4.6 years ago, created an answer that was upvoted at least 5 times. For A: Illumina Read Names: /2 Vs. /3
Teacher 4.6 years ago, created an answer with at least 3 up-votes. For A: Shall We Go Back To Stackexchange?
Teacher 4.8 years ago, created an answer with at least 3 up-votes. For A: Shall We Go Back To Stackexchange?
Appreciated 5.0 years ago, created a post with more than 5 votes. For A: Shall We Go Back To Stackexchange?
Popular Question 5.1 years ago, created a question with more than 1,000 views. For Duplication And Quality Control In Published Ngs Data

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