How to compile Alignment Report from bam.summary.txt file

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Overview

In some cases, an RNASeq Pipeline run encounters an issue and cannot complete all steps, or some samples failed during the alignment, requiring a re-run for those failed samples. In these cases, a merged Alignment Report will not be generated for all of the samples in the final project. This wiki will show users how to manually compile the bam.summary.txt file to get the whole alignment report.

Merge text files

The bam.summary.txt file will be generated after the alignment in the output folder with Bam file, if they are on server folder, please download the text file to local folder.

User can merge these text file by going to Tools | Data | Merge Text Files:

Alignmentreport1.png

Use Add to load these text files, and in the options, check the mark for Ignore first line and Do not ignore the firstfile:

Alignmentreport2.png

After clicking OK, user can save the merged text file in the local drive:

Alignmentreport3.png

Load merged text file to ArrayStudio

Once the text files got merged, user can upload the merged table to server folder, then they can open the server project and load the table like this:

Alignmentreport4.png

Alignmentreport5.png

Alignmentreport6.png

Transpose the table

Once the table loaded to ArrayStudio, user can transpose the table to have a table like Alignment report exactly:

Alignmentreport7.png

For more information regarding the transpose, user can refer to the Table function for Transpose Table.


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