Question: RSEM on single replicate with multiple fasta files
gravatar for gozrom
2.6 years ago by
gozrom80 wrote:

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 • 1.2k views
ADD COMMENTlink modified 2.6 years ago • written 2.6 years ago by gozrom80
gravatar for swbarnes2
2.6 years ago by
United States
swbarnes29.1k wrote:

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

ADD COMMENTlink written 2.6 years ago by swbarnes29.1k

Thanks, that seems to work...

ADD REPLYlink modified 2.6 years ago • written 2.6 years ago by gozrom80
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