Hello Everyone,
I have made bam files using hisat2 and then I am trying to use these bam files for salmon alignment.
hisat2-build genome.fa hisat
hisat2 -x hisat -1 R1_paired.fastq.gz -2 R2_paired.fastq.gz -S out.sam
samtools view -bS out.sam > out.bam
java -Xms1g -Xmx3g -jar picard.jar MarkDuplicates
I=out.bam
O=marked_duplicates.bam
M=metrics.txt
salmon quant -t transcripts.fasta -l A -a marked_duplicates.bam -o out.sf
But it gives an error:
Please provide a reference FASTA file that includes all targets present in the BAM header
If you have access to the genome FASTA and GTF used for alignment
consider generating a transcriptome fasta using a command like:
gffread -w output.fa -g genome.fa genome.gtf
Thank you for any help!