Hi!
I have run bracer test and have different results, but there is no error when testing. Is it common?
my results:
BCR_H reconstruction: 2 / 3 (66.7%)
BCR_K reconstruction: 0 / 3 (0.0%)
BCR_L reconstruction: 3 / 3 (100.0%)
Paired HK productive reconstruction: 0 / 3 (0.0%)
Paired HL productive reconstruction: 2 / 3 (66.7%)
Paired KL productive reconstruction: 0 / 3 (0.0%)
+--------+----------------+---------------+----------------+
| | 0 recombinants | 1 recombinant | 2 recombinants |
+--------+----------------+---------------+----------------+
| all H | 1 | 2 (100%) | 0 (0%) |
| all K | 2 | 1 (100%) | 0 (0%) |
| all L | 0 | 3 (100%) | 0 (0%) |
| prod H | 1 | 2 (100%) | 0 (0%) |
| prod K | 3 | 0 (N/A%) | 0 (N/A%) |
| prod L | 0 | 3 (100%) | 0 (0%) |
+--------+----------------+---------------+----------------+
##Cells with more than two recombinants for a locus##
The following cells are likely multiplets or contaminated as they contain more than two recombinants for a locus. Consider removing them from downstream analysis.
None
##Proportion of full-length sequences of all recovered sequences##
H K L
all 2/2 (100%) 1/1 (100%) 3/3 (100%)
prod 2/2 (100%) 0/0 (N/A%) 3/3 (100%)
##Isotype of cells with productive heavy chain##
Isotype cells % of cells
IGHA1 2 100.00
#Clonotype groups#
This is a text representation of the groups shown in clonotype_network_with_identifiers.pdf.
It does not exclude cells that only share heavy chain and not light chain if Summarise is run with --IGH_networks.
cell2, cell3
#Cells with no reconstructed sequences#
None
expected results:
BCR_H reconstruction: 3 / 3 (100.0%)
BCR_K reconstruction: 0 / 3 (0.0%)
BCR_L reconstruction: 3 / 3 (100.0%)
Paired HK productive reconstruction: 0 / 3 (0.0%)
Paired HL productive reconstruction: 3 / 3 (100.0%)
Paired KL productive reconstruction: 0 / 3 (0.0%)
+--------+----------------+---------------+----------------+
| | 0 recombinants | 1 recombinant | 2 recombinants |
+--------+----------------+---------------+----------------+
| all H | 0 | 3 (100%) | 0 (0%) |
| all K | 2 | 1 (100%) | 0 (0%) |
| all L | 0 | 3 (100%) | 0 (0%) |
| prod H | 0 | 3 (100%) | 0 (0%) |
| prod K | 3 | 0 (N/A%) | 0 (N/A%) |
| prod L | 0 | 3 (100%) | 0 (0%) |
+--------+----------------+---------------+----------------+
##Cells with more than two recombinants for a locus##
The following cells are likely multiplets or contaminated as they contain more than two recombinants for a locus. Consider removing them from downstream analysis.
None
##Proportion of full-length sequences of all recovered sequences##
H K L
all 3/3 (100%) 1/1 (100%) 2/3 (67%)
prod 3/3 (100%) 0/0 (N/A%) 2/3 (67%)
##Isotype of cells with productive heavy chain##
Isotype cells % of cells
IGHA1 2 66.67
IGHG1 1 33.33
#Clonotype groups#
This is a text representation of the groups shown in clonotype_network_with_identifiers.pdf.
It does not exclude cells that only share heavy chain and not light chain if Summarise is run with --IGH_networks.
cell2, cell3
#Cells with no reconstructed sequences#
None
test log:
56438 reads; of these:
56438 (100.00%) were paired; of these:
35350 (62.64%) aligned concordantly 0 times
21088 (37.36%) aligned concordantly exactly 1 time
0 (0.00%) aligned concordantly >1 times
----
35350 pairs aligned concordantly 0 times; of these:
73 (0.21%) aligned discordantly 1 time
----
35277 pairs aligned 0 times concordantly or discordantly; of these:
70554 mates make up the pairs; of these:
69268 (98.18%) aligned 0 times
232 (0.33%) aligned exactly 1 time
1054 (1.49%) aligned >1 times
38.63% overall alignment rate
56438 reads; of these:
56438 (100.00%) were paired; of these:
56438 (100.00%) aligned concordantly 0 times
0 (0.00%) aligned concordantly exactly 1 time
0 (0.00%) aligned concordantly >1 times
----
56438 pairs aligned concordantly 0 times; of these:
0 (0.00%) aligned discordantly 1 time
----
56438 pairs aligned 0 times concordantly or discordantly; of these:
112876 mates make up the pairs; of these:
112876 (100.00%) aligned 0 times
0 (0.00%) aligned exactly 1 time
0 (0.00%) aligned >1 times
0.00% overall alignment rate
56438 reads; of these:
56438 (100.00%) were paired; of these:
48319 (85.61%) aligned concordantly 0 times
8119 (14.39%) aligned concordantly exactly 1 time
0 (0.00%) aligned concordantly >1 times
----
48319 pairs aligned concordantly 0 times; of these:
114 (0.24%) aligned discordantly 1 time
----
48205 pairs aligned 0 times concordantly or discordantly; of these:
96410 mates make up the pairs; of these:
95663 (99.23%) aligned 0 times
195 (0.20%) aligned exactly 1 time
552 (0.57%) aligned >1 times
15.25% overall alignment rate
56438 reads; of these:
56438 (100.00%) were paired; of these:
31766 (56.28%) aligned concordantly 0 times
24672 (43.72%) aligned concordantly exactly 1 time
0 (0.00%) aligned concordantly >1 times
----
31766 pairs aligned concordantly 0 times; of these:
270 (0.85%) aligned discordantly 1 time
----
31496 pairs aligned 0 times concordantly or discordantly; of these:
62992 mates make up the pairs; of these:
61549 (97.71%) aligned 0 times
144 (0.23%) aligned exactly 1 time
1299 (2.06%) aligned >1 times
45.47% overall alignment rate
[build] loading fasta file /Personal/zhouxin/software/bracer/test_data/results/cell1/expression_quantification/kallisto_index/cell1_transcriptome.fa
[build] k-mer length: 31
[build] warning: clipped off poly-A tail (longer than 10)
from 1827 target sequences
[build] warning: replaced 4 non-ACGUT characters in the input sequence
with pseudorandom nucleotides
[build] counting k-mers ... done.
[build] building target de Bruijn graph ... done
[build] creating equivalence classes ... done
[build] target de Bruijn graph has 1510231 contigs and contains 142452662 k-mers
[quant] fragment length distribution will be estimated from the data
[index] k-mer length: 31
[index] number of targets: 231,959
[index] number of k-mers: 142,452,662
[index] number of equivalence classes: 990,749
[quant] running in paired-end mode
[quant] will process pair 1: /Personal/zhouxin/software/bracer/test_data/cell1_1.fastq
/Personal/zhouxin/software/bracer/test_data/cell1_2.fastq
[quant] finding pseudoalignments for the reads ... done
[quant] processed 56,438 reads, 41,888 reads pseudoaligned
[quant] estimated average fragment length: 135.93
[ em] quantifying the abundances ... done
[ em] the Expectation-Maximization algorithm ran for 246 rounds
/SGRNJ/Public/Software/conda_env/Bracer/lib/python3.7/site-packages/seaborn/distributions.py:2557: FutureWarning: `distplot` is a deprecated function and will be removed in a future version. Please adapt your code to use either `displot` (a figure-level function with similar flexibility) or `histplot` (an axes-level function for histograms).
warnings.warn(msg, FutureWarning)
/SGRNJ/Public/Software/conda_env/Bracer/lib/python3.7/site-packages/seaborn/distributions.py:306: UserWarning: Dataset has 0 variance; skipping density estimate.
warnings.warn(msg, UserWarning)
/SGRNJ/Public/Software/conda_env/Bracer/lib/python3.7/site-packages/seaborn/distributions.py:2557: FutureWarning: `distplot` is a deprecated function and will be removed in a future version. Please adapt your code to use either `displot` (a figure-level function with similar flexibility) or `histplot` (an axes-level function for histograms).
warnings.warn(msg, FutureWarning)
Hi! I have run bracer test and have different results, but there is no error when testing. Is it common? my results:
expected results:
test log:
thank you!