Dear all, hope you all are doing well,
I have assembled the transcriptome data of Tagetes erecta Leaf (SRR7641101) and Tagetes erecta flower (SRR7641100) by using Trinity assembler. Now I want to do differential gene expression analysis of the same and was running RSEM to generate count matrix by the following command...
/mnt/c/Users/Delluser/Desktop/NGS/Trinityrnaseq-v2.6.6/util/align_and_estimate_abundance.pl --seqType fq \ --transcripts /mnt/d/RSEM/Trinity.fasta \ --left /mnt/d/RSEM/Tagetes_erecta_SRR7641101_Leaf/TAGETESL_2.fastq.gz \ --right /mnt/d/RSEM/Tagetes_erecta_SRR7641101_Leaf/trim_TAGETESL_1.fastq.gz \ --est_method RSEM \ --aln_method bowtie \ --trinity_mode \ --prep_reference \ --output_dir /mnt/d/RSEM/RSEM_Leaf
And after running the above command I'm getting an error which is as follows...
[E::sam_hrecs_update_hashes] Duplicate entry "TRINITY_DN4744_c0_g1_i1" in sam header samtools view: failed to add PG line to the header samtools sort: failed to read header from "-" Error while flushing and closing output Error, cmd: set -o pipefail && bowtie -q --all --best --strata -m 300 --chunkmbs 512 -X 800 -S -p 4 /mnt/d/RSEM/Trinity.fasta.bowtie -1
Get headers from the Trinity.fasta file and check the duplication.
If it has a duplicate remove any one of the sequences.
- Badges
- Science topic
- Similar topics
- Correction