Query related to RSEM

Question

[bioinformatics.queries]

Hi

I am running RSEM for the first time. In the command for the expression it says as follow

rsem-calculate-expression --phred64-quals \
                           -p 8 \
                           --output-genome-bam \
                           /data/mmliver.fq \
                           /ref/mouse_125 \
                           mmliver_single_quals

Could anyone tell me what is this mmliver_single_quals stands for? When I am trying to run the command it terminated without showing any error. I used the following command

./rsem-calculate-expression  --phred64-quals  -p 8   --gzipped-read-file  293TInput2_S21_L008_R1_001.fastq.gz    /ref/human_gencode  /NOR.sequences/293T

I shall be very thankful for your response.

Answer 1

[swbarnes2]

It looks like the last element in the command line when structured like that is just what prefix will be added to all the output files, so you can control what they are called.

[bioinformatics.queries]

I have used the following command but it terminated without running

./rsem-calculate-expression  --phred64-quals   -p 8   --gzipped-read-file /data/shilpia2/NOR.sequences/293T/293TInput2_S21_L008_R1_001.fastq.gz   /data/shilpia2/ref/human_gencode  /data/shilpia2/NOR.sequences/293T/293T

can anyone tell me what could be the problem?

[Ram]

1. When you're replying to someone who answered you, saying "can anyone ..." is unprofessional. You're replying to them asking them for further help - not making an announcement standing in their proximity. Imagine you extend your hand to someone that fell in a ditch, they then look at your face and shout back "Someone please help me".
2. Please use the formatting bar (especially the code option) to present your post better. You can use backticks for inline code (`text` becomes text), or select a chunk of text and use the highlighted button to format it as a code block. I've done it for you this time.