Output format
Mclumi provides three output files after running each of the dedup_basic, dedup_pos, dedup_gene, and dedup_sc modules, with the following names.
{method}_ave_ed_pos_bin.txt{method}_dedup_sum.txt{name}_dedup.bam
Please note that {method} above refers to {uniq}, {cc}, {adj}, {direc}, {mcl}, {mcl_val}, or {mcl_ed} standing for the unique, adjacency, directional, mcl, mcl_val, or mcl_ed method, correspondingly. {name} can be designated by users. Result format is spelt out below.
1. Single genomic position/gene/gene-by-cell result format
After running module dedup_basic, the results will be stored in a {method}_ave_ed_pos_bin.txt file and a {method}_dedup_sum.txt file indicating deduplicated UMI counts across all reads in a given bam file.
2. Genomic position result format
{method}_ave_ed_pos_bin.txt
Data at the third row is interpreted as: the number of genomic positions observed with an average edit distance 3 between UMIs is 4.
edit distance |
number |
|---|---|
-1.0 |
3652 |
2.0 |
1 |
3.0 |
4 |
… |
… |
the 1st column: average edit distance between UMIs at genomic positions
the 2nd column: number of gene-by-cell types observed with those average edit distance, respectively
-1.0 represents that only one unique umi seen at a single genomic position; in total there are 3652 genomic positions seen with one unique umi.
{method}_dedup_sum.txt
No. |
{met hod}_u mi_len |
a ve_ eds |
uniq_ umi_len |
dedup_ uniq_diff_pos |
dedup_ read_diff_pos |
|---|---|---|---|---|---|
0 |
4 |
4.0 |
4 |
0 |
0 |
1 |
2 |
5.0 |
2 |
0 |
0 |
2 |
7 |
4.0 |
9 |
2 |
2 |
… |
… |
… |
… |
… |
… |
the 1st column: genomic positions of interest
the 2nd column: deduplicated UMI counts (corresponding to the number of DNA molecules/transcripts) at genomic positions
the 3rd column: average edit distances between UMIs at given genomic positions
the 4th column: unique UMI counts at given genomic positions
the 5th column: difference in dedup UMI counts and original unique UMI counts
the 6th column: difference in the number of dedup reads and original reads
3. bulk RNA-seq result format
{method}_ave_ed_pos_bin.txt
Spelling out results
Data at the third row is interpreted as: the number of gene types observed with an average edit distance 3 between UMIs is 4.
edit distance |
number |
|---|---|
-1.0 |
3652 |
2.0 |
1 |
3.0 |
4 |
… |
… |
the 1st column: average edit distance between UMIs at gene types
the 2nd column: number of gene types observed with those average edit distances, respectively
-1.0 represents that only one unique umi seen at a single gene type; in total there are 3652 genomic positions seen with one unique umi.
{method}_dedup_sum.txt
the 1st column: gene types
the 2nd column: deduplicated UMI counts (corresponding to the number of DNA molecules/transcripts) at a given gene type
the 3rd column: average edit distances between UMIs at given gene types
the 4th column: unique UMI counts at given gene types
the 5th column: difference in dedup UMI counts and original unique UMI counts
the 6th column: difference in the number of dedup reads and original reads
4. scRNA-seq data format
Data at the third row is interpreted as: the number of gene-by-cell types observed with an average edit distance 3 between UMIs is 4.
{method}_ave_ed_pos_bin.txt
edit distance |
number |
|---|---|
-1.0 |
3652 |
2.0 |
1 |
3.0 |
4 |
… |
… |
the 1st column: average edit distance between UMIs at gene-by-cell types
the 2nd column: number of gene-by-cell types observed with those average edit distances, respectively
{method}_dedup_sum.txt
type |
{ metho d}_um i_len |
a v e _ e d s |
uniq _umi _len |
d edup_uniq _diff_pos |
d edup_read _diff_pos |
|---|---|---|---|---|---|
(‘AAAGATGAGAAACGAG’, ‘exon-NM_000099.4-3’) |
6 |
0 |
6 |
0 |
0 |
(‘AAAGATGAGAAACGAG’, ‘exon-NM_000100.4-3’) |
14 |
0 |
14 |
0 |
0 |
(‘AAAGATGAGAAACGAG’, ‘exon-NM_000101.4-6’) |
3 |
0 |
3 |
0 |
0 |
… |
… |
… |
… |
… |
… |
the 1st column: gene-by-cell types
the 2nd column: dedup UMI counts (corresponding to the number of DNA molecules/transcripts) at given gene-by-cell types
the 3rd column: average edit distance between UMIs at gene-by-cell types
the 4th column: average edit distance between UMIs at given gene-by-cell types
the 5th column: unique UMI counts at given gene-by-cell types
the 6th column: difference in dedup UMI counts and original unique UMI counts
the 7th column: difference in the number of dedup reads and original reads