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  • What's the consequence of using only one lane

    Hi All,

    I am currently analyzing an RNA-Seq experiment which consists of two conditions, control and treatment. Each condition has 3 biological replicates. For each bio. reps., the samples are sequenced in 2 lanes, so I got two accepted_hits.bam files using TopHat, one from each lane.

    My question is, I think using 2 lanes is just to increase the sequencing depth, so we can use samtools merge to combine the two BAM files into a single one and then continue to analyze. However, because I will be comparing different methods for isoform detections, and some methods require different inputs, which makes "file merging" rather difficult (say, merge BED files...). I wonder if it is possible to just focus on 1 lane for each biological sample, at the cost of reduced sequencing depth (only)?

    Thanks for your suggestions!

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