RSEM on single replicate with multiple fasta files
Entering edit mode
3.1 years ago
gozrom ▴ 80

Hi, there,

I'm running RSEM on 12 replicates each replicate has 8 fasta files, paired-end reads.

This is inside 2 For loops with i from 1 to 4 and j from 1 to 4

rsem-calculate-expression -p 8 --bowtie2 --paired-end --strandedness forward --append-names --estimate-rspd --output-genome-bam ~/RNAseq/RSEM_fasta/control-"$i"*_L00"$j"_R1_001.fastq.gz ~/RNAseq/RSEM_fasta/control-"$i"*_L00"$j"_R2_001.fastq.gz  ~/RNAseq/ref/mouse_ensemble ~/RNAseq/RSEM/Control"$i"/sample_"$j"

This command will generate 4 fasta files of single replicate,

is there a way to create a combined one file that includes results from all 4 fasta files for a single replicate

I used this previously For loop with i running from 1 to 12 and j running from 1 to 4 but then I realized that each time it creates a new file with the same name and doesn't really combine with the previous one. So at the end I have files for the last two fasta files for each sample (that's my guess).

rsem-calculate-expression -p 8 --bowtie2 --paired-end --strandedness forward --append-names --estimate-rspd --output-genome-bam ~/RNAseq/RSEM_fasta/*S"$i"*_L00"$j"_R1_001.fastq.gz ~/RNAseq/RSEM_fasta/*-"$i"*_L00"$j"_R2_001.fastq.gz  ~/RNAseq/ref/mouse_ensemble ~/RNAseq/RSEM/sample_"$i"

I still want to combine all fasta files for each replicate into one file and then all those files for 12 replicates into one file

Is there a nice way to do it with RSEM?

Thank you.

RNA-Seq • 1.3k views
Entering edit mode
3.1 years ago
swbarnes2 9.9k

Why can't you cat the files together before putting them in RSEM? Catting gzipped fastq files works fine.

Entering edit mode

Thanks, that seems to work...


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