diff --git a/docs/mixcr/reference/pics/data-qc/alignment_absent_barcode.png b/docs/mixcr/reference/pics/data-qc/alignment_absent_barcode.png deleted file mode 100644 index f7254d61..00000000 Binary files a/docs/mixcr/reference/pics/data-qc/alignment_absent_barcode.png and /dev/null differ diff --git a/docs/mixcr/reference/pics/data-qc/alignment_absent_barcode.svg b/docs/mixcr/reference/pics/data-qc/alignment_absent_barcode.svg new file mode 100644 index 00000000..57747a85 --- /dev/null +++ b/docs/mixcr/reference/pics/data-qc/alignment_absent_barcode.svg @@ -0,0 +1,428 @@ + + + + + + + + + + + 0 + + + + + + + 10 + + + + + + + 20 + + + + + + + 30 + + + + + + + 40 + + + + + + + 50 + + + + + + + 60 + + + + + + + 70 + + + + + + + 80 + + + + + + + 90 + + + + + + + 100 + + + + + + + + + + + DChu_PBMC_wrong_pattern.vdjca + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Alignments rate + + + + + + + + + + % + + + + + + + + + + + + + + + + + + + + + + + Successfully aligned + + + + + + + + + + + + + + + + + + + No hits (not TCR/IG?) + + + + + + + + + + + + + + + + + + + No CDR3 parts + + + + + + + + + + + + + + + + + + + No V hits + + + + + + + + + + + + + + + + + + + No J hits + + + + + + + + + + + + + + + + + + + No target with both V and J + + + + + + + + + + + + + + + + + + + Low total score + + + + + + + + + + + + + + + + + + + Absent barcode + + + + + + + + \ No newline at end of file diff --git a/docs/mixcr/reference/pics/data-qc/alignment_not_TCR_IG.png b/docs/mixcr/reference/pics/data-qc/alignment_not_TCR_IG.png deleted file mode 100644 index fd2648a4..00000000 Binary files a/docs/mixcr/reference/pics/data-qc/alignment_not_TCR_IG.png and /dev/null differ diff --git a/docs/mixcr/reference/pics/data-qc/alignment_not_TCR_Ig.svg b/docs/mixcr/reference/pics/data-qc/alignment_not_TCR_Ig.svg new file mode 100644 index 00000000..ed3935f5 --- /dev/null +++ b/docs/mixcr/reference/pics/data-qc/alignment_not_TCR_Ig.svg @@ -0,0 +1,428 @@ + + + + + + + + + + + 0 + + + + + + + 10 + + + + + + + 20 + + + + + + + 30 + + + + + + + 40 + + + + + + + 50 + + + + + + + 60 + + + + + + + 70 + + + + + + + 80 + + + + + + + 90 + + + + + + + 100 + + + + + + + + + + + mice_IFNg_trb_example.vdjca + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Alignments rate + + + + + + + + + + % + + + + + + + + + + + + + + + + + + + + + + + Successfully aligned + + + + + + + + + + + + + + + + + + + No hits (not TCR/IG?) + + + + + + + + + + + + + + + + + + + No CDR3 parts + + + + + + + + + + + + + + + + + + + No V hits + + + + + + + + + + + + + + + + + + + No J hits + + + + + + + + + + + + + + + + + + + No target with both V and J + + + + + + + + + + + + + + + + + + + Low total score + + + + + + + + + + + + + + + + + + + Absent barcode + + + + + + + + \ No newline at end of file diff --git a/docs/mixcr/reference/qc-repseq.md b/docs/mixcr/reference/qc-repseq.md index b321f195..7900da77 100644 --- a/docs/mixcr/reference/qc-repseq.md +++ b/docs/mixcr/reference/qc-repseq.md @@ -29,7 +29,7 @@ Before considering different reasons in more details, the general advice is to c Alignment report shows the reasons why your reads are not aligned. Let's consider them in more detail. -![](pics/data-qc/alignment_not_TCR_IG.png) +![](pics/data-qc/alignment_not_TCR_Ig.svg) ### Alignment failed, no hits (not TCR/IG?) @@ -69,7 +69,7 @@ Finally, it might be a wrong use of the analysis preset: if the input data is ra ### Absent barcode -![](pics/data-qc/alignment_absent_barcode.png) +![](pics/data-qc/alignment_absent_barcode.svg) For barcoded data means that barcodes can't be extracted using the specified [tag pattern](ref-tag-pattern.md). The first thing to check is that a correct tag pattern and/or a correct [analysis preset](overview-built-in-presets.md) are used. If the library is unstranded, one should use either `--tag-parse-unstranded` option or change the preset accordingly. Finally, the quality of data may be low, so that tags can't be parsed because of too many sequencing errors. @@ -222,8 +222,72 @@ mixcr exportAlignmentsPretty -n 10 path/to/vdjca/file ``` Here `-n 10` option limits the number of alignments in the output. +``` +>>> Read ids: 8 + +>>> Tags: +>>> UMI: TTTGATTACGGTTT FGGGGGGGGGGGGC + + + FR1> + L L I L * F Y Y L G L G T L + Quality 132322122335622352225466764461312315413411 + Target0 237 CTTTTGATCCTTTAGTTTTATTATTTGGGCCTGGGAACCCTG 278 Score +IGHV3-30*00 463 AGtAATaCAc 472 914 + + + _ Q C R F T I Y R D T S Q K T L Y L Q M N S L T L E D + Quality 11211335463422145142162115143134441651667764543155445566653445533155757663324776 + Target1 0 GCAGTGCCGATTCACCATCTACAGAGACACTTCCCAGAAGACGCTGTATCTGCAGATGAACAGCCTGACACTTGAGGACA 79 Score +IGHV3-30*00 348 gAagGgccgattcaccatctCcagagacaAttccAagaaCacgctgtatctgcaAatgaacagcctgaGaGCtgaggaca 427 720 + + FR3>