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Assembly Procedure

The document outlines the assembly procedure which includes creating directories, moving files, editing scripts, submitting jobs to a queue, and checking status. Key steps are to create a project directory, move raw data files, edit mapping scripts, submit mapping jobs, and monitor logs.

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emilio
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19 views

Assembly Procedure

The document outlines the assembly procedure which includes creating directories, moving files, editing scripts, submitting jobs to a queue, and checking status. Key steps are to create a project directory, move raw data files, edit mapping scripts, submit mapping jobs, and monitor logs.

Uploaded by

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

1. if the project dir does not exist


mkdir /storage/DATA_RAW/ERP10142

2. if data file are places into different folder


mv ERR863675.sra ERR863676.sra ERR863677.sra ERR863678.sra
ERR863679.sra /storage/DATA_RAW/ERP10142

3. create script copy for your test


cp mapping_SGE_SRP029880.sh mapping_SGE_ERR863675.sh

4. edit the new script


vi mapping_SGE_ERR863675.sh

5. set DATA_DIR correctly and save changes mapping_SGE_ERR863675.sh*

6. create copy of mapping reads submission file


cp mapping_readsSRP029880.sh mapping_readsERR863675.sh

7. edit the new file mapping_readsERR863675.sh


vi mapping_readsERR863675.sh

8. set the correct execution file (the script created with *) and save changes

9. open screen session qsub


screen [ENTER]

10 submit to serial96.q queue specifying the COMMENT_ARG and SRA_NAME.


For example:
qsub -q serial96.q mapping_readsERR863675.sh TUMOR_ERP10142
ERR863675

11. Or, if you need to get the list of SRA files to assembly
ls /storage/DATA_RAW/SRP052896 | awk -F "." '{printf $1" "}'

Then you will have the a list like the following

SRR975551 SRR975552 SRR975554 SRR975555 SRR975556 SRR975558 SRR975560 SRR975563

You can submit using

for i in SRR975551 SRR975552 SRR975554 SRR975555 SRR975556 SRR975558


SRR975560 SRR975563 ; do qsub -q serial96.q mapping_read.sh
Tumor_SRP029880 $i; done

11. check about status with qstat and log file


qstat -j 1823 ; tail -f mapping_reads.log

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