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2 hours ago by

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!

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modified 2 hours ago

by

Rob3.7k

written
2 hours ago
by

evelyn90



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