Get that to the BMC

stela2502 · Nov 14, 2023 · 272d4fb · 272d4fb
1 parent 4fd60b4
commit 272d4fb
Showing 1 changed file with 8 additions and 0 deletions.
diff --git a/idenitfy_index_failing_reads.sh b/idenitfy_index_failing_reads.sh
@@ -1,2 +1,10 @@
 target/release/quantify_rhapsody -r testData/cells.1.Rhapsody_SV_index1_S1_R1_001.fastq.gz -f testData/cells.1.Rhapsody_SV_index1_S1_R2_001.fastq.gz -o testData/BD_results/Rustody_S1 -s mouse  -e testData/2276_20220531_chang_to_rpl36a_amplicons.fasta -a testData/MyAbSeqPanel.fasta -m 200 -v v2.96 > testData/BD_results/Rustody_S1/mapped_reads.txt
 target/release/quantify_rhapsody -r testData/cells.1.Rhapsody_SV_index1_S1_R1_001.fastq.gz -f testData/cells.1.Rhapsody_SV_index1_S1_R2_001.fastq.gz -o testData/BD_results/Rustody_S1 -s mouse  -e testData/2276_20220531_chang_to_rpl36a_amplicons.fasta -a testData/MyAbSeqPanel.fasta -m 200 -v v2.96 > testData/BD_results/Rustody_S1/mapped_reads.txt
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+Rscript idenitfy_index_failing_reads.R
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+zgrep -f R1_ids_not_in_index.txt testData/cells.1.Rhapsody_SV_index1_S1_R1_001.fastq.gz -A3 | sed '/--/d' | gzip > testData/failing_in_index_cells.1.Rhapsody_SV_index1_S1_R1_001.fastq.gz
+zgrep -f R2_ids_not_in_index.txt testData/cells.1.Rhapsody_SV_index1_S1_R2_001.fastq.gz -A3 | sed '/--/d' | gzip > testData/failing_in_index_cells.1.Rhapsody_SV_index1_S1_R2_001.fastq.gz
+
+
+target/release/quantify_rhapsody_multi -r testData/failing_in_index_cells.1.Rhapsody_SV_index1_S1_R1_001.fastq.gz -f testData/failing_in_index_cells.1.Rhapsody_SV_index1_S1_R2_001.fastq.gz -o testData/BD_results/Rustody_S1 -s mouse  -e testData/2276_20220531_chang_to_rpl36a_amplicons.fasta -a testData/MyAbSeqPanel.fasta -m 200 -v v2.96