'analysis_barcodes.py': add options for truncating extracted index sequences before analysis - #1188
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… sequences. Adds new options --i1_length and --i2_length which can be used to specify the lengths that the I1 and I2 index sequences should be truncated to for analysis.
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Updates the
bin/analyse_barcodes.pyutility to add new options--i1_lengthand--i2_length, which can be used to specify the lengths that the I1 and I2 index sequences extracted from the FASTQ read headers should be truncated to.For example: if the read header looks like:
then by default the extracted index sequence will be be
AAATCCAGAC+CACAACATTC(using the format<I1>+<I2>).The new options can be used to transform the sequences prior to analysis, for example
--i1_length=6would transform the sequence to:and
--i2_length=0would transform it to a single index sequence:This is intended to help with troubleshooting the sample demultiplexing post-FASTQ generation in specific cases where multiple projects appear in a single sequencer lane with different indexing schemes (for example to check whether expected indexes from the non-default indexing scheme are present in the "undetermined" reads).