Hello, I am trying to do a RNA-Seq on a mouse cell line derived from a mouse strain that is different from the strain used to generate the reference genome (mm9 or mm10).
Is there an alignment software that does need a reference genome? I checked Kallisto but it does not generate BAM files. Thanks.
You will need to clarify what you want. I understood you want to align using a reference transcriptome and obtain a bam mapping, though it is not clear if a reference transcriptome built from your own reads, or one derived from the standard reference genome and annotation. If you do not want to align to a transcriptome and instead want something else, you will have to spell out clearly what you want.
Do you want to align to a reference transcriptome, and obtain bam files? Salmon can do that, as BWA or Bowtie.
Do you want to assemble a reference transcriptome (with Trinity / Velvet+Oases / etc) from your reads, align the reads to it and obtain a bam file? Again, Salmon, BWA or Bowtie can do that.
With STAR, you can align to a reference genome and output the mapping to the transcriptome.
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version 2.3.6
"that need a reference genome" Or "does not need" ?
Genome guided assembler : Cufflinks, Stringtie, bayesembler, etc... => sam/bam output
De-novo assembler : Trinity, Oases, SOAPdenovo-Trans, etc... => fasta output
This sounds like a good job for HISAT2 / StringTie, but by using the pre-existing reference genome FASTA and transcriptome GTF as guides. This would allow you to see the intricate differences in transcript expression between your strain and the reference.
Kallisto does produce BAMs, or, should I say 'pseudo-bams'.