File Content Explanation Query​

[XiaoxiaoZhang2]

Hello, I have downloaded some RNA-seq blood junction data using the package recount3. In the files, does the number in the first column of gtex.junctions.BLOOD.ALL.MM correspond to the row number minus 1 in the file gtex.junctions.BLOOD.ALL.RR, and does the sample ID in the second column also match the order of different samples in files like qc?

[XiaoxiaoZhang2]

Hello, let me elaborate on my inquiry.

For example, the downloaded junction-related file junctions.BLOOD.ALL.MM.gz contains the following first three lines of data (excluding comments):

4690652 1048 210126607
1 572 1
2 821 1

Here, it can be seen that there are 4,690,652 junction events and 1,048 blood samples. I would like to know which specific junctions correspond to the event IDs 1 and 2, and which samples correspond to the sample IDs 572 and 821. I have not found explanations for this in the existing results or software parameters.

The positional information for junction events in the file junctions.BLOOD.ALL.RR.gz looks like this:

chromosome start end length strand annotated left_motif right_motif left_annotated right_annotated
ERCC-00002 73 127 55 + 0 GT AG 0 0
ERCC-00002 494 576 83 - 0 CT AC 0 0

I would like to know whether the order of junction events in this file corresponds to the event IDs in junctions.BLOOD.ALL.MM.gz.
Similarly, the order in the file junctions.BLOOD.ALL.ID.gzis sorted by rail_idin ascending order. Does this ordering also correspond to the sample IDs in junctions.BLOOD.ALL.MM.gz?

However, the sorting in the file recount_project.BLOOD.MD.gz appears as follows:

rail_id external_id study project organism file_source metadata_source date_processed
2183552 GTEX-111YS-0006-SM-5NQBE.1 BLOOD BLOOD Homo sapiens data_sources/gtex data_sources/gtex 2019-11-01
2298319 GTEX-1122O-0003-SM-5Q5DL.1 BLOOD BLOOD Homo sapiens data_sources/gtex data_sources/gtex 2019-11-01

The sample order in this file seems to follow a different arrangement. How exactly can I determine the corresponding junction events and samples for the event IDs and sample IDs in junctions.BLOOD.ALL.MM.gz?

I am quite confused about this and would greatly appreciate your clarification.