How to interpreat the output data

[dhwani2410]

I am able to run all the code but not able to interpret the output and make any conclusion from it. I checked the FuSeq manual but the output of FuSeq-WGS seems bit different from the FuSeq.

Can you please share a link where it can read about the output and its interpretations like for

In "feq_ALL.txt" what does "Read and Freq" column mean
What does "MR" and "SR" pipeline mean
why are all scores of fusionDB "0"

Please suggest link to read about output

[Trung Nghia Vu]

hi @dhwani2410,

feq_ALL.txt reports all fusion equivalence classes (feqs) from the data. In this file, column Feq indicates the index of feqs where the rows with the same feq contain the information of the "transcripts" belonging to the eqclass. Column Count expresses the number of reads supporting the feq. Column Read is a flag for the previous step to extract the discordant reads, however this column is not used for downstream processing.

Throughout the pipeline, MR and SR indicate mapped reads (discordant reads) and split reads.

We used the Mitelman fusion database to check if the discovered fusions exist in the database or not. fusionDB=0 indicates that fusion is not found in that database.

I summarize the files in the output folder as follows:

• feq_ALL.txt: raw output of discordant reads (MR) in fusion equivalence classes
• splitReadInfo.txt: raw output of split reads (SR)
• FuSeq_WES_MR_fge.txt: fusion genes from the mapped reads (MR fusions) after the post-processing steps
• FuSeq_WES_MR_fge_fdb.txt: the MR fusions but keep only fusion overlapping with the Mitelman fusion database
• FuSeq_WES_SR_fge.txt: fusion genes from the split reads (SR fusions) after the post-processing steps
• FuSeq_WES_SR_fge_fdb.txt: the SR fusions but keep only fusion overlapping with the Mitelman fusion database
• FuSeq_WES_FusionFinal.txt: the combination of MR fusions and SR fusions

If the filters/test in the post-processing steps are too strict, some interesting fusions might be missing. In this case, one can investigate them in the raw outputs of SR and MR.

I hope this would help to make clear the output of FuSeq_WES.

Nghia