Hello everyone,
I have paired-end fastq files from different lanes. When is it most appropriate to merge them during a transcriptomic analysis?
The files are named like: File_condition1_R1_L001.fastq, File_condition1_R2_L001.fastq, File_condition1_R1_L002.fastq, File_condition1_R2_L002.fastq, etc.
I used HISAT2 and generated BAM files, then I merged the BAM files from the same sample but from different lanes (ex. File_condition1_R1_L001.bam and File_condition1_R1_L002.bam).
After that, I sorted the merged BAM files using Samtools.
Is this correct? Do you have any suggestions or opinions on the best method to work with the same sample from different lanes?
Thank you very much in advance.
1 answer
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As long as you did the alignments using the paired files you can merge the BAM files for lanes for a sample afterwards.
But if you aligned the reads independently i.e. R1/R2 independently then that would be wrong. You always want to align the read-pairs for a sample together.
Yes, sorry, my mistake. I meant to say that I used R1 and R2 of a sample, generated the BAM, and then merged the BAM files from different lanes for the same sample. On the merged BAM files, I then performed sorting and indexing. Is that correct?