๐Ÿ  ไธป้กต โ€ข English

๐Ÿงฌ DNBelab C Series HT scVDJ ๅˆ†ๆžๆต็จ‹

ๅ•็ป†่ƒž VDJ ๆต‹ๅบๆ•ฐๆฎๅˆ†ๆžๅฎŒๆ•ดๆŒ‡ๅ—

๐Ÿ“‹ ๆฆ‚่ฟฐ โ€ข ๐Ÿ“ ๆ–‡ไปถๅ‡†ๅค‡ โ€ข ๐Ÿš€ ไธปๅˆ†ๆžๆต็จ‹ โ€ข ๐Ÿ“Š ็ป“ๆžœ่งฃๆž

๐Ÿ“‹ ๆฆ‚่ฟฐ

ๆœฌๆ–‡ๆกฃ่ฏฆ็ป†ไป‹็ปไบ†ไฝฟ็”จ dnbc4tools ่ฟ›่กŒๅ•็ป†่ƒž VDJ ๆต‹ๅบๆ•ฐๆฎๅˆ†ๆž็š„ๅฎŒๆ•ดๆต็จ‹ใ€‚

ๅทฅไฝœๆต็จ‹๏ผš5็ซฏ่ฝฌๅฝ•็ป„ๅˆ†ๆž โ†’ VDJๆ–‡ๅบ“ๅค„็† โ†’ ๅบๅˆ—็ป„่ฃ…ๆณจ้‡Š โ†’ ็ป†่ƒž่ฟ‡ๆปค โ†’ ๅ…‹้š†ๅž‹ๅˆ†ๆž โ†’ ๅˆ†ๆžๆŠฅๅ‘Š

ๅทฅไฝœๆต็จ‹ๅ›พ
๐Ÿ’ก ไฝฟ็”จ่ฏดๆ˜Ž๏ผš$dnbc4tools ไปฃ่กจๅฏๆ‰ง่กŒ็จ‹ๅบ่ทฏๅพ„๏ผŒไฝฟ็”จๆ—ถ้œ€่ฆๆ›ฟๆขไธบๅฎž้™…ๅฎ‰่ฃ…่ทฏๅพ„ใ€‚ๆข่กŒ็ฌฆ `\` ็”จไบŽๅœจๅ‘ฝไปค่กŒไธญๅฐ†ๅ‘ฝไปคๅˆ†ไธบๅคš่กŒ๏ผŒไปฅๆ้ซ˜ๅฏ่ฏปๆ€งใ€‚

๐Ÿ“ ๆ–‡ไปถๅ‡†ๅค‡

5็ซฏ่ฝฌๅฝ•็ป„ๅˆ†ๆž

่ฝฌๅฝ•็ป„ๅˆ†ๆž่ฏทๅ‚่€ƒ dnbc4tools rna runใ€‚5'็ซฏ่ฝฌๅฝ•็ป„ๅˆ†ๆžไธปๆต็จ‹้œ€ๅœจๅ•็ป†่ƒžRNAไธปๆต็จ‹ๅˆ†ๆžๅŸบ็ก€ไธŠๆทปๅŠ ๅ‚ๆ•ฐ --end5ใ€‚

ไธบๅ•ไธชๆ ทๆœฌ็”Ÿๆˆ่กจ่พพ็Ÿฉ้˜ต๏ผŒไปฅไธ‹ๆ˜ฏไธ€ไธช็คบไพ‹ๆญฅ้ชคๆˆ–่„šๆœฌๆจกๆฟ๏ผš

$dnbc4tools rna run \
	--name sample_5rna \
	--cDNAfastq1 /data/sample_cDNA_R1.fastq.gz \
	--cDNAfastq2 /data/sample_cDNA_R2.fastq.gz \
	--oligofastq1 /data/sample_oligo1_1.fq.gz,/data/sample_oligo2_1.fq.gz \
	--oligofastq2 /data/sample_oligo1_2.fq.gz,/data/sample_oligo2_2.fq.gz \
	--genomeDir /opt/database/Homo_sapiens \
	--threads 30 \
	--end5
โš ๏ธ ๆณจๆ„๏ผš5็ซฏ่ฝฌๅฝ•็ป„ๅˆ†ๆžๆ˜ฏVDJๅˆ†ๆž็š„ๅ‰ๆ๏ผŒ้œ€่ฆๅ…ˆๅฎŒๆˆๆญคๆญฅ้ชคๆ‰่ƒฝ่ฟ›่กŒๅŽ็ปญๅˆ†ๆžใ€‚

VDJๅˆ†ๆžๆ‰€้œ€ๆ–‡ไปถ

ๅˆ†ๆž้œ€่ฆไปฅไธ‹ๆ–‡ไปถ๏ผš

ๆ–‡ไปถ็ฑปๅž‹ ่ฏดๆ˜Ž
FASTQๆ–‡ไปถ VDJๆ–‡ๅบ“ๆต‹ๅบๆ•ฐๆฎ๏ผŒๅŒ…ๅซTCRๆˆ–BCRๅบๅˆ—ไฟกๆฏ
singlecell.csvๆ–‡ไปถ 5็ซฏ่ฝฌๅฝ•็ป„ๅˆ†ๆž็ป“ๆžœไธญ็š„็ป†่ƒžไฟกๆฏๆ–‡ไปถ

ๅˆ†ๆž้œ€่ฆ5'็ซฏ่ฝฌๅฝ•็ป„ๅˆ†ๆž็ป“ๆžœ็›ฎๅฝ•ไธญ็š„ singlecell.csv ๆ–‡ไปถใ€‚่ฏฅๆ–‡ไปถๅŒ…ๅซ cell ๅ’Œ barcode ๅˆ—็š„ๅˆๅนถไฟกๆฏ๏ผŒไปฅๅŠ is_cell_barcode ๅˆ—๏ผˆ1่กจ็คบ็ป†่ƒž๏ผŒ0่กจ็คบ้ž็ป†่ƒž๏ผ‰๏ผŒ็”จไบŽ้‰ดๅฎšๆœ‰ๆ•ˆ็š„็ป†่ƒžใ€‚

โš ๏ธ ๆณจๆ„๏ผš็กฎไฟsinglecell.csvๆ–‡ไปถ่ทฏๅพ„ๆญฃ็กฎ๏ผŒ่ฏฅๆ–‡ไปถๆ˜ฏ่ฟžๆŽฅ่ฝฌๅฝ•็ป„ๅ’ŒVDJๅˆ†ๆž็š„ๅ…ณ้”ฎใ€‚

ๅ‚่€ƒ็คบไพ‹ๆ–‡ไปถๅ†…ๅฎน๏ผš

cell,reads,gene,umi,is_cell_barcode,barcode
CELL1118_N3,1485813,5693,57580,1,AGATCGCCTACGATCACGAT;GGTGGAAGGTGAGAGAAGCG;GTAGTTCTAGGCTAAGTACT
CELL1651_N3,805447,4881,32131,1,ATCTCAAGCCCACCGTGTGT;CATCAATTAAGTGATCGCAT;CCTAACTGAGGAACGCTTAG
CELL4_N3,820269,5649,30326,1,AACACCTGATCGTTCAATAA;AATTCGAAGGTAGTCGGAAT;CACATGTTACATGTTCTATA
CELL906_N3,656624,4853,28142,1,ACGTCCGCGTGACCATGTGC;AGGAGCTCCATTGATCTTAA;CAATCCGGAGAACGTATCTG
CELL1577_N2,672637,4610,24822,1,ATATTCTCACGTAACGGATG;TAGGAACTCGGCTTAGATCT
CELL2064_N2,542608,2355,23324,1,CATAAGCACTCACCGCTAGT;GTCTCACAGTTGTTCACTAG
CELL1332_N6,580950,4702,22953,1,AGGTGTAAGCCTACCGGACC;CGCACTCACCTAACATTGTG;CTTGCCGCGCTATCAATGCA;GCCACTAGTCGACGCGGTTG;GTCAGCATGCTCTTCCACAG;TCGATATCCTCACTCTTAAC
CELL726_N4,585934,4617,22660,1,ACCTACGGCGTTACTATGTG;CGACGCTCTCGACAGTTAGG;CGGCAGAGTCTTGGCGCTTA;TCCGACCGTATCTTCATCTC
CELL4010_N1,555308,4268,22554,1,AGAGAGTCGCAGCAAGCGAC

๐Ÿš€ ไธปๅˆ†ๆžๆต็จ‹

VDJไธปๅˆ†ๆžๆต็จ‹็ป“ๅˆไบ†ๅ•็ป†่ƒžVDJๆ–‡ๅบ“ๆต‹ๅบๆ•ฐๆฎๅ’Œๅฏนๅบ”ๆ ทๆœฌ็š„5'่ฝฌๅฝ•็ป„ๅˆ†ๆž็ป“ๆžœ๏ผŒๅŒ…ๅซไปฅไธ‹ๅ…ณ้”ฎๆญฅ้ชค๏ผš

  1. ๅฏนๆ•ฐๆฎ่ฟ›่กŒ่ฟ‡ๆปค๏ผŒๅˆฉ็”จ 5' ่ฝฌๅฝ•็ป„็ป“ๆžœๅˆๅนถ็ฃ็ 
  2. ๆฏ”ๅฏน VDJ ๅŸบๅ› ๅŒบๅŸŸๅนถๆๅ–ๅฏนๅบ”็š„ reads
  3. ่ฟ›่กŒไปŽๅคด็ป„่ฃ…ๅนถๆณจ้‡Š
  4. ๆ นๆฎ็ป„่ฃ…ๆณจ้‡Š็ป“ๆžœๅ’Œ 5' ่ฝฌๅฝ•็ป„็š„็ป†่ƒž่Žทๅ–ๆƒ…ๅ†ต่ฟ›่กŒ็ป†่ƒž่ฟ‡ๆปค
  5. ๆ•ดๅˆๅ„ๆญฅ้ชค็ป“ๆžœ็”Ÿๆˆ HTML ็ฝ‘้กตๆŠฅๅ‘Šๅนถ่พ“ๅ‡บๅˆ†ๆž็ป“ๆžœ

TCRๅˆ†ๆž

ไธบๅ•ไธชๆ ทๆœฌ่ฟ่กŒTCRๅˆ†ๆž๏ผŒไปฅไธ‹ๆ˜ฏไธ€ไธช็คบไพ‹ๆญฅ้ชคๆˆ–่„šๆœฌๆจกๆฟ๏ผš

$dnbc4tools vdj run \
	--name sample_tcr \
	--fastq1 /data/sample_tcr_R1.fastq.gz \
	--fastq2 /data/sample_tcr_R2.fastq.gz \
	--ref human \
	--chain TR \
	--beadstrans /sample_5rna/outs/singlecell.csv \
	--threads 10

BCRๅˆ†ๆž

ไธบๅ•ไธชๆ ทๆœฌ่ฟ่กŒBCRๅˆ†ๆž๏ผŒไปฅไธ‹ๆ˜ฏไธ€ไธช็คบไพ‹ๆญฅ้ชคๆˆ–่„šๆœฌๆจกๆฟ๏ผš

$dnbc4tools vdj run \
	--name sample_bcr \
	--fastq1 /data/sample_bcr_R1.fastq.gz \
	--fastq2 /data/sample_bcr_R2.fastq.gz \
	--ref human \
	--chain IG \
	--beadstrans /sample_5rna/outs/singlecell.csv \
	--threads 10

่ฟ่กŒ่ฟ‡็จ‹

ๅœจๅฏนๆš—ๅๅบ”่‡ชๅŠจๆฃ€ๆต‹ๅŽ๏ผŒ่ฝฏไปถๅผ€ๅง‹่ฟ่กŒๅˆ†ๆž๏ผŒไปฅไธ‹ๆ˜ฏไธ€ไธช็คบไพ‹๏ผš

โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€ Parsed FASTQ Inputs โ€” 2025-11-12 15:13:16 โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€
โ”Œโ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”ฌโ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”
โ”‚ Type  โ”‚ Path                                                                                     โ”‚
โ”œโ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”ผโ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”ค
โ”‚ Read1 โ”‚ /data/test_ATAC_R1.fastq.gz                                                              โ”‚
โ”‚ Read2 โ”‚ /data/test_ATAC_R2.fastq.gz                                                              โ”‚
โ””โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”ดโ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”˜
โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€


โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€ Chemistry Detection โ€” 2025-11-12 15:13:20 โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€
โ”Œโ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”ฌโ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”
โ”‚ Type                            โ”‚ Result                                                         โ”‚
โ”œโ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”ผโ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”ค
โ”‚ Read1                           โ”‚ darkreaction                                                   โ”‚
โ””โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”ดโ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”˜
โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€โ”€

 2025-11-12 15:13:20 Starting VDJ library filtering...                                              
...done

 2025-11-12 15:15:46 Preparing input data for VDJ assembly...                                       
...done

 2025-11-12 15:18:14 Performing VDJ sequence assembly and gene segment annotation...                
...done

 2025-11-12 16:03:18 Performing cell calling for VDJ data...                                        
...done

 2025-11-12 16:04:02 Generating VDJ clonotype analysis...                                           
...done

 2025-11-12 16:05:02 Converting VDJ results from cellbarcode to cell ID...                          
...done

 2025-11-12 16:05:15 Generating analysis report and summary statistics...                           
...done

Analysis Finished Elapsed Time: 0:52:24

ๆˆๅŠŸ็š„่ฟ่กŒไผšไปฅ Analysis Finished ็ป“ๆŸใ€‚

๐Ÿ“Š ็ป“ๆžœ่งฃๆž

ๅˆ†ๆžๅฎŒๆˆๅŽ๏ผŒๅฐ†็”Ÿๆˆ็ป“ๆžœ่พ“ๅ‡บ็›ฎๅฝ•outs๏ผŒlogsๆ—ฅๅฟ—็›ฎๅฝ•๏ผŒๅ…ถไธญouts็›ฎๅฝ•ๅŒ…ๆ‹ฌ๏ผš

. 
โ”œโ”€โ”€ airr_annotations.tsv
โ”œโ”€โ”€ all_contig_annotations.csv
โ”œโ”€โ”€ all_contig.fasta
โ”œโ”€โ”€ all_contig.fasta.fai
โ”œโ”€โ”€ *_scVDJ_IG_report.html
โ”œโ”€โ”€ clonotypes.csv
โ”œโ”€โ”€ consensus_annotations.csv
โ”œโ”€โ”€ consensus.fasta
โ”œโ”€โ”€ consensus.fasta.fai
โ”œโ”€โ”€ filtered_contig_annotations.csv
โ”œโ”€โ”€ filtered_contig.fasta
โ”œโ”€โ”€ filtered_contig.fasta.fai
โ””โ”€โ”€ metrics_summary.xls

็›ธๅ…ณๆ–‡ๆกฃ๏ผš

โ“ ๅธธ่ง้—ฎ้ข˜

ๅ†…ๅฎนๅพ…่กฅๅ