Compare revisions

Daniel Heß · Daniel Heß · 19b5a342 · 19b5a342 · 19b5a342 · d284f05e
--- a/.gitattributes
+++ b/.gitattributes
@@ -3,4 +3,5 @@ assays/rnaseq/dataset/DH_RNA_Nodules_S19_R1_001.fastq.gz filter=lfs diff=lfs mer
 *.xlsx diff=ssdiff merge=binary
 **/dataset/**/* filter=lfs diff=lfs merge=lfs -text
 *.fq.gz filter=lfs diff=lfs merge=lfs -text
-
+**/dataset/** filter=lfs diff=lfs merge=lfs -text
+runs/ppl14025-sup-0002-table.xlsx filter=lfs diff=lfs merge=lfs -text
--- a/assays/Fragmentanalyzer/isa.assay.xlsx
+++ b/assays/Fragmentanalyzer/isa.assay.xlsx
--- a/assays/Nanodrop/isa.assay.xlsx
+++ b/assays/Nanodrop/isa.assay.xlsx
--- a/assays/rnaseq/dataset/DH_RNA_Nodules_S19_R1_001.fastq.gz
+++ b/assays/rnaseq/dataset/DH_RNA_Nodules_S19_R1_001.fastq.gz
--- a/assays/rnaseq/isa.assay.xlsx
+++ b/assays/rnaseq/isa.assay.xlsx
--- a/assays/rnaseq/protocols/AnalysisNGSlibPool_Shimadzu.PNG
+++ b/assays/rnaseq/protocols/AnalysisNGSlibPool_Shimadzu.PNG
--- a/assays/rnaseq/protocols/SeqDataDeliveryNote_Abbreviation.txt
+++ b/assays/rnaseq/protocols/SeqDataDeliveryNote_Abbreviation.txt
+Sequence Data Delivery Note
+VProject VB2275 
+15.10.2022
+The NGS libraries (2 samples) were single-read sequenced on an Illumina NextSeq 500 system using 75 bp read length.
+
+Summary of sequencing Run:
+Total Reads 	130.024.459
+Cluster(PF) 	116.060.162
+% Cluster 	89,3
+Reads ident. 	107.465.709
+% Index 	92,6
+
+Sample ID Sample Name Barcode i5 Barcode i7 Number of Reads
+1 DH_RNA_Nodules CAAGTGGG TCCGCGAA DH_RNA_Nodules_S19_R1_001.fastq.gz 54.042.636
+2 DH_RNA_Control AGATTTGG TCCGCGAA DH_RNA_Control_S20_R1_001.fastq.gz 53.423.073
+
+The NGS library pool was analysed on a Shimadzu MultiNA microchip electrophoresis system.
+
--- a/assays/rnaseq/protocols/cDNA_LibraryPrep_Vertis_Protocol.pdf
+++ b/assays/rnaseq/protocols/cDNA_LibraryPrep_Vertis_Protocol.pdf
--- a/assays/rnaseq/protocols/herebeprotocol.txt
+++ b/assays/rnaseq/protocols/herebeprotocol.txt
--- a/isa.investigation.xlsx
+++ b/isa.investigation.xlsx
--- a/runs/BEAST/alignment_files/g31563_select.fasta
+++ b/runs/BEAST/alignment_files/g31563_select.fasta
--- a/runs/BEAST/alignment_files/g41182_select.fasta
+++ b/runs/BEAST/alignment_files/g41182_select.fasta
--- a/runs/BEAST/alignment_files/pap11_align_name.fasta
+++ b/runs/BEAST/alignment_files/pap11_align_name.fasta
--- a/runs/BEAST/alignment_files/pap11_clustalw_aln.txt
+++ b/runs/BEAST/alignment_files/pap11_clustalw_aln.txt
--- a/runs/BEAST/xml_files/1e6_pap11align_name.xml
+++ b/runs/BEAST/xml_files/1e6_pap11align_name.xml
--- a/runs/BEAST/xml_files/g31563_g41182_1mil.xml
+++ b/runs/BEAST/xml_files/g31563_g41182_1mil.xml
--- a/runs/BEAST/xml_files/g41182_select_1e6.xml
+++ b/runs/BEAST/xml_files/g41182_select_1e6.xml
--- a/runs/herebeBEASTruns.txt
+++ b/runs/herebeBEASTruns.txt
--- a/runs/herebegalaxyanalysis.txt
+++ b/runs/herebegalaxyanalysis.txt
--- a/assays/rnaseq/dataset/DH_RNA_Control_S20_R1_001.fastq.gz
+++ b/assays/rnaseq/dataset/DH_RNA_Control_S20_R1_001.fastq.gz
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