I got this error while trying to do salmon from an aligned bam file. The bam file is an output of tophat from paired end fastq file.
WARNING: Detected suspicious pair ---
The names are different:
read1 : SRR2103637.12484815
read2 : SRR2103637.12492049
The proper-pair statuses are inconsistent:
read1 [SRR2103637.12484815] : proper-pair; mapped; matemapped
read2 : [SRR2103637.12484815] : no proper-pair; mapped; matemapped
My salmon command is:
salmon quant -t ../idx/Ch38.cdna.all.fa -l IU -a sorted.bam -g ../gene_map.txt -o salmon_out
I tried both unsorted bam and sorted bam and both resulted the same warning.
My questions is:
1. What can I do to fix this or I can just ignore it?
2. For libtype parameter in Salmon, how to choose the correct parameter? How can I check whether it is inward, backward, or matching and stranded of not stranded? Can I check from the fastq files or it has something to check from the experiment itself? I downloaded the data from NCBI GEO and it said it is from Illumina HiSeq2500 100bp paired-end mode of the TruSeq Rapid PE Cluster kit and TruSeq Rapid SBS kit (Illumina)
Thank you for your answer and suggestion.