Problems with fragment length distribution output with Salmon
New to RNA-Seq and I’m struggling with my Salmon alignment output. I tried to find an answer to this question on older posts but I couldn’t locate any other discussions, so apologies in advance if this has been covered before.
My data is from Illumina 150 bp pair-end reads (5 control samples, 5 drug-treated). Using Salmon for alignment, I first created an index file with the reference transcriptome from NCBI (fasta format) and then ran each of my pair of fastq files against this reference index file. An example of the code is shown below.
salmon_quant -i reference_transcriptome -lA -1 fastq_1 -2 fastq_2 -o ouput_file_name --gcBias
When checking my output in MULTIQC, my ‘Fragment Length Distribution’ is primarily located around 300 bp, when i’ve been informed this should be around 150 bp. Previous data from the lab using Salmon with 100 bp and 150 bp pair-end reads showed the distribution around the 100 and 150 bp mark, so I’m confused as to why mine is predominantly located around the 300 bp range.
Any suggestions on why this is? Is there something wrong/missing from my code? The image from my MULTIQC is shown below
Thanks in advance!
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