Scribd
Upload
3 views1 page

Step-by-Step Assembly Procedure Guide

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
3 views1 page

Step-by-Step Assembly Procedure Guide

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

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 [Link] [Link] [Link] [Link]
[Link] /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

You might also like