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luke831215 / SQUAT

a Sequencing Quality Assessment Tool
GNU General Public License v3.0
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R1 and R2 fastq files #6

Open ghost opened 4 years ago

ghost commented 4 years ago

It was recommended on the instructions to combine paired-end reads (R1 and R2) into a single file. Could you clarify if this is to combine/concatenate them into one file (i.e. cat R1.fastq R2.fastq > Output.fastq), interleave them (via BBMap) or join the overlaps (via FLASH, fastq-join).

hiruna72 commented 4 years ago

In their paper it is mentioned as below,

Paired-end version and 10X data So far, only single-end read mapping is available for SQUAT. Namely, no paired-end information is required. In BWA, we can also generate alignments in SAM format given paired-end libraries. However, a different scheme of read label tagging and analysis needs to be designed to fit interleaved read files into the process. In the future, we will place the emphasis on quality assessment of paired-end reads. The current version of SQUAT can perform quality assessment of 10X chromatin-linked reads and the assembly, but it ignores paired-end barcode information. We plan to support paired-end 10X linked reads with barcode analysis.

So, I guess the paired-end reads should be interleaved.