I'm trying to use RSEM for a paired-end data to map it against human reference with STAR aligner. After, trimming the adapter sequences with cutadapt, when I try to align the reads with RSEM, with the following command;
rsem-calculate-expression -p 6 --paired-end --phred64-quals --output-genome-bam --star --star-path /home/Downloads/tools/STAR-2.5.3a/source --estimate-rspd --append-names sample1-R1_trimmed.fastq sample1-R2_trimmed.fastq ref_genome/human_ref sample1.expression
I get this error;
Warning: Read A00902:595:HC27FDRX2:2:2226:26476:24236 is ignored due to at least one of the mates' length < seed length (= 25)!
How can I solve this issue? Is this because the adapter trimming is not done correctly? Or there is some issue with the input RSEM commands I used?