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Ido Tamir
Ido Tamir
Role:
Moderator
Reputation:
5,240
Joined:
15.1 years ago
Last seen:
3.1 years ago
Location:
Austria

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

 

Latest posts by user
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Comment: Comment: Trust in BQSR for AVITI
written by Ido Tamir Ido Tamir
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Trust in BQSR for AVITI
aviti bqsr
written by Ido Tamir Ido Tamir
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Answer: Answer: RnBeads SLURM submission problem.
written by Ido Tamir Ido Tamir
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Comment: C: How to fill with dots empty fields in a dataframe in R when splitting a column b
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Comment: C: Data management in R, perl or python
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Answer: A: New data transformation tool for Windows and Mac
written by Ido Tamir Ido Tamir
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Comment: C: how to get total read count, mapped read count and unmapped read count from mult
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Comment: C: RNA-Seq and no of reads
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Comment: C: Running a code in batch mode on a list of files
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Comment: C: Extracting rows on basis of specific column values in R
written by Ido Tamir Ido Tamir
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Comment: C: Trouble with choosing the right reference transcriptome file for mm10
written by Ido Tamir Ido Tamir
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Answer: A: RNA-Seq differential gene expression without biological and technical replicates
written by Ido Tamir Ido Tamir
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Answer: C: How to get DE genes without replicates using EdgeR
written by Ido Tamir Ido Tamir
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Comment: C: How many of the reads end up being counted by HTSeq count
written by Ido Tamir Ido Tamir
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Answer: A: How many of the reads end up being counted by HTSeq count
written by Ido Tamir Ido Tamir
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Comment: C: D' and r2 graphics in R
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Comment: C: How can I extract the sequencing reads containing a specific linker/tag?
written by Ido Tamir Ido Tamir
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Answer: A: How can I extract the sequencing reads containing a specific linker/tag?
written by Ido Tamir Ido Tamir
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Answer: A: Adding annotations to the bam file from the txt file
written by Ido Tamir Ido Tamir
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Comment: C: problem installing cutadapt
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