Category Archives: bioinformatics

How to select genomic region using samtools

Posted on December 15, 2022 by Thomas Cokelaer

To select a genomic region using samtools, you can use the faidx command. This command is used to index a FASTA file and extract subsequences from it. Here is an example of how to use faidx to select a genomic … Continue reading →

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conda list command broken (unknown variable: python_implementation)

Posted on July 26, 2021 by Thomas Cokelaer

Recently I had my conda environment raising a long error report when calling conda list One of the relevant error message refers to an unknown variable python_implementation. raise SyntaxError(‘unknown variable: %s’ % expr) File “”, line None SyntaxError: unknown variable: … Continue reading →

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All about RNA and DNA sequencing

Posted on August 8, 2018 by Thomas Cokelaer

Great entry with description of RNA and DNA sequencing: enseqlopedia

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missing SAM header with minimap2 and samtools

Posted on May 15, 2018 by Thomas Cokelaer

When using minimap2 to map sequencing reads onto a reference, you can use this kind of command (be careful, this is wrong as you will see later): minimap2 -a -x map-pb test.fastq reference.fasta > minimap.samminimap2 -a -x map-pb test.fastq reference.fasta … Continue reading →

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failed to convert from cram to bam (parse error CIGAR character)

Posted on January 10, 2018 by Thomas Cokelaer

In order to convert a bioinformatic file from CRAM to BAM format, I naively used the samtools command available on a cluster but got this error: samtools view -T reference.fa -b -o output.bam input.cram [sam_header_read2] 3366 sequences loaded. [sam_read1] reference … Continue reading →

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