summary file

[daixiaozhuan]

Hi Junchao,

I want to generate the ratio of different RNA types. Firstly, I extracted the information directly from the file "*.mapped.sorted.txt" in the "processing_report" folder. But I check the reads number is not correct. Then I checked the summary file as below, why the Match_Genome number is larger than the Clean_Reads? Do you have any advice on which file should I use the output the summary?

Thanks, Xiaozhuan

[junchaoshi]

It's not a normal result. Could you check the processing log file to see if everything works fine?

[daixiaozhuan]

Hi,

There is no error information in the log file.

Is it because of the multi-mapping reads? I checked several samples, which all have the same problem.

Xiaozhuan

[daixiaozhuan]

Hi,

This is the command that I used as below:

Xiaozhuan

[junchaoshi]

I mean the log file in the processing_report folder since you performed the -k parameter.

[daixiaozhuan]

It only has one txt file as below:

[junchaoshi]

Since there are warnings in the processing file, please make sure your input files and/or the reference files are valid.

[daixiaozhuan]

I checked the input and reference. But I didn't find any error. By the way, I want to make sure that I use the result in the "processing_report" to report the ratio of different small RNA types. Is it correct?

[junchaoshi]

Since there are warnings in the processing file, something should be wrong with your processing step. The ratio in the processing file represents the unique species of the total species aligned rather than the reads ratio.

[daixiaozhuan]

If I want to know the reads ratio. Then which file should I use?

[daixiaozhuan]

There are warnings because I used the reads that only can mapped to genome. So the unmapped genome part is empty.

[junchaoshi]

The reads of each type of small RNA and each sequence are in the [sample_name]_output.txt and [sample_name]_summary.txt which are in the [sample_name]_reusult folder. You do not need to remove genome_unmapped reads before annotation. The genome mapping information is already included in the result folder. And it may cause incorrect counting, as you asked at the beginning.

[junchaoshi]

Please read the README file carefully, the instruction of each output file is already included.