I've ran RSEM on my data and saw alignment rate of around 2%
Example: "3134964 reads; of these:
3134964 (100.00%) were paired; of these:
3054835 (97.44%) aligned concordantly 0 times
52834 (1.69%) aligned concordantly exactly 1 time
27295 (0.87%) aligned concordantly >1 times
2.56% overall alignment rate"
I've aligned this data using hisat2 with the same full mouse genome file and the alignment rate was >90%, doing it on Galaxy with Hisat also resulted with >90% alignment rate.
I used bowtie2 in RSEM command to generate alignment based on the index built by bowtie2 also using RSEM:
This was used to build the index:
rsem-prepare-reference --gtf $genes --bowtie2 ~/RNAseq/RSEM/Mus_musculus.GRCm38.dna.chromosome.1.fa ~/RNAseq/ref/mouse_ensemble
And this was used to run RSEM within the for loop:
rsem-calculate-expression -p 8 --bowtie2 --paired-end --strandedness forward --append-names --estimate-rspd --output-genome-bam ~/RNAseq/RSEM/c_all/Control"$i"_R1.fastq.gz ~/RNAseq/RSEM/c_all/CTRL"$i"_R2.fastq.gz ~/RNAseq/ref/mouse_ensemble ~/RNAseq/RSEM/c_all/RSEM/Control"$i"
ArnonMe
commented
4 years ago
Hi, there,
I've ran RSEM on my data and saw alignment rate of around 2% Example: "3134964 reads; of these: 3134964 (100.00%) were paired; of these: 3054835 (97.44%) aligned concordantly 0 times 52834 (1.69%) aligned concordantly exactly 1 time 27295 (0.87%) aligned concordantly >1 times 2.56% overall alignment rate"
I've aligned this data using hisat2 with the same full mouse genome file and the alignment rate was >90%, doing it on Galaxy with Hisat also resulted with >90% alignment rate.
I used bowtie2 in RSEM command to generate alignment based on the index built by bowtie2 also using RSEM:
This was used to build the index: rsem-prepare-reference --gtf $genes --bowtie2 ~/RNAseq/RSEM/Mus_musculus.GRCm38.dna.chromosome.1.fa ~/RNAseq/ref/mouse_ensemble
And this was used to run RSEM within the for loop: rsem-calculate-expression -p 8 --bowtie2 --paired-end --strandedness forward --append-names --estimate-rspd --output-genome-bam ~/RNAseq/RSEM/c_all/Control"$i"_R1.fastq.gz ~/RNAseq/RSEM/c_all/CTRL"$i"_R2.fastq.gz ~/RNAseq/ref/mouse_ensemble ~/RNAseq/RSEM/c_all/RSEM/Control"$i"
I've looked online to check this issue found a google group discussion. https://groups.google.com/forum/#!topic/rsem-users/3RiF4WneNw0
Did not find it helpful.
I'm trying to understand if that what it is suppose to be in the report, there are no separate files with unaligned reads....