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Procedure To Count RPKM Using CONIFER: For I in 'Find Tumor - ERP10142 - ERR8636 - Name ' RPKM'' Do LL $i Done

1. Submit jobs to multiple computer nodes to run the counting_reads.sh script on folders containing sequencing data to generate RPKM files. 2. Check the status of submitted jobs using the qstat command. 3. Verify that the RPKM file was generated in each folder and is not empty. 4. Extract the first line of each RPKM file, prepending the sample name, and save to a single output file called Tumor_SRP029880_rpkm.

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emilio
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20 views

Procedure To Count RPKM Using CONIFER: For I in 'Find Tumor - ERP10142 - ERR8636 - Name ' RPKM'' Do LL $i Done

1. Submit jobs to multiple computer nodes to run the counting_reads.sh script on folders containing sequencing data to generate RPKM files. 2. Check the status of submitted jobs using the qstat command. 3. Verify that the RPKM file was generated in each folder and is not empty. 4. Extract the first line of each RPKM file, prepending the sample name, and save to a single output file called Tumor_SRP029880_rpkm.

Uploaded by

emilio
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
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Download as PDF, TXT or read online on Scribd
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Procedure to count RPKM

using CONIFER

1. apply counting_reads.sh over all folders containing results


for i in {551..600}; do qsub -q serial96.q counting_reads.sh
Tumor_SRP029880_SRR975$i ; done

Or if you have the same list as before:

for i in SRR975551 SRR975552 SRR975554 SRR975555 SRR975556


SRR975558 SRR975560 SRR975563 SRR975564 SRR975567 SRR975571
SRR975574 SRR975575 SRR975576 SRR975580 SRR975582 SRR975585
SRR975586 SRR975587 SRR975588 SRR975589 SRR975591 SRR975593
SRR975598 SRR975599 ;do qsub -q serial96.q counting_reads.sh
Tumor_SRP029880_$i; done

2. check submission using qstat

3. check that every folder contains its rpkm file not empty
for i in `find Tumor_ERP10142_ERR8636* -name '*rpkm'`; do ll
$i ; done

4. save value about the 1st exome for every rpkm file into a unique
file
for i in {551..600}; do echo -n "SRR975$i ">>
Tumor_SRP029880_rpkm ; head -n 1
Tumor_SRP029880_SRR975$i/SRR975$i"_"rpkm >>
Tumor_SRP029880_rpkm; done

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