-
Notifications
You must be signed in to change notification settings - Fork 2
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
- Added new trimming method (`bbduk`) for tiling experiment - Added new adapters for tiling - Removed R dependency `stringr` and `stringi` #7
- Loading branch information
Showing
30 changed files
with
638 additions
and
264 deletions.
There are no files selected for viewing
File renamed without changes.
File renamed without changes.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,98 @@ | ||
| >H1pdmHA_0_LEFT | ||
| GAGCAAAAGCAGGGGAAAACA | ||
| >H1pdmHA_1_LEFT_me | ||
| TCTGCTGTATACATTTACAACCGC | ||
| >H1pdmHA_1_LEFT_me_alt1 | ||
| TCTGCTGTATACATTCACAACCGC | ||
| >H1pdmHA_1_LEFT_me_alt2 | ||
| TCTACTGTGTACATTTACAACCGC | ||
| >H1pdmHA_2_LEFT_new | ||
| GGTAGCCCCATTGCATTTGG | ||
| >H1pdmHA_3_LEFT | ||
| ACAATGGAACGTGTTACCCAGG | ||
| >H1pdmHA_4_LEFT | ||
| GTGTAACGGCAGCATGTCCT | ||
| >H1pdmHA_4_LEFT_alt1 | ||
| GTGTAACGGCAGCATGTTCT | ||
| >H1pdmHA_4_LEFT_alt2 | ||
| GTGTAACAGCAGCATGTCCT | ||
| >H1pdmHA_5_LEFT | ||
| AAAGGGAAAGAAGTCCTCGTGC | ||
| >H1pdmHA_6_LEFT | ||
| GGGATCAAGAAGGGAGAATGAACT | ||
| >H1pdmHA_7_LEFT | ||
| TGCAATACAACTTGTCAGACACC | ||
| >H1pdmHA_7_LEFT_alt1 | ||
| TGCAATACAACTTGTCAGACCCC | ||
| >H1pdmHA_8_LEFT | ||
| CAATCTAGAGGCCTATTCGGGG | ||
| >H1pdmHA_8_LEFT_alt1 | ||
| TCAATCTAGAGGCCTATTTGGGG | ||
| >H1pdmHA_9_LEFT | ||
| AGAGCACACAAAATGCCATTGA | ||
| >H1pdmHA_9_LEFT_alt1 | ||
| AGAGCACACAGAATGCCATTGA | ||
| >H1pdmHA_10_LEFT | ||
| CCTGGACATTTGGACTTACAATGC | ||
| >H1pdmHA_11_LEFT | ||
| TGCTTTGAATTTTACCACAAATGCG | ||
| >H1pdmHA_last_LEFT | ||
| ACCCAAAATACTCAGAGGAAGCA | ||
| >H1pdmNA_0_LEFT | ||
| CAGCAAAAGCAGGAGTTTAAAATGAA | ||
| >H1pdmNA_0_LEFT_alt1 | ||
| AGCAAAAGCAGGAGTTTTAAAATGAA | ||
| >H1pdmNA_2_LEFT | ||
| TGAAACATGCAATCAAAGCGTCAT | ||
| >H1pdmNA_2_LEFT_alt1 | ||
| TTGAAACATGCAATAAAAGCGTCAT | ||
| >H1pdmNA_2_LEFT_alt2 | ||
| CAGATTGAAACATGCAATAAAAACGTCAT | ||
| >H1pdmNA_3_LEFT | ||
| AGTGGATGGGCTATATACACTAAAGAC | ||
| >H1pdmNA_3_LEFT_alt1 | ||
| AGTGGATGGGCTATATACAGTAAAGAC | ||
| >H1pdmNA_4_LEFT_me | ||
| TCGAACCCTAATGAGCTGTCC | ||
| >H1pdmNA_4_LEFT_me_alt1 | ||
| CGAACCCTAATGAGCTGCCC | ||
| >H1pdmNA_5_LEFT | ||
| GGCATAATAACAGACACTATCAAGAGTT | ||
| >H1pdmNA_6_LEFT | ||
| CATACAAGATCTTCAGAATAGAAAAGGGAA | ||
| >H1pdmNA_6_LEFT_alt1 | ||
| TCATACAAAATCTTCAGAATAGAAAAGGGAA | ||
| >H1pdmNA_6_LEFT_alt2 | ||
| CCTCATACAAAATCTTCAGAATAGAAAAAGGAA | ||
| >H1pdmNA_7_LEFT | ||
| AATCGACCGTGGGTGTCTTT | ||
| >H1pdmNA_8_LEFT_new2 | ||
| ATACGGCAATGGTGTTTGGATAG | ||
| >H1pdmNA_last_LEFT_new | ||
| GTATAAGACCTTGCTTCTGGGTTG | ||
| >A-M-UniF | ||
| GGGGGGAGCAAAAGCAGGTAG | ||
| >H1pdmMP_1_LEFT | ||
| GAGGCTCTCATGGAATGGCTA | ||
| >H1pdmMP_2_LEFT_me | ||
| TGACTAAGGGGATTTTAGGGTTTGT | ||
| >H1pdmMP_2_LEFT_me_alt1 | ||
| CTCTGACTAAGGGAATTTTAGGATTTGT | ||
| >H1pdmMP_2_LEFT_me_alt2 | ||
| TCTGACTAAGGGGATTTTAGGATTTGT | ||
| >H1pdmMP_3_LEFT_new_alt1 | ||
| CCAAGGAGGTGTCACTAAGCT | ||
| >H1pdmMP_3_LEFT_new_alt2 | ||
| GCCAAAGAAGTGTCACTAAGCT | ||
| >H1pdmMP_4_LEFT_me | ||
| CTGATTCACAGCATCGGTCTCA | ||
| >H1pdmMP_5_LEFT | ||
| CTGGATCAAGTGAACAGGCAG | ||
| >H1pdmMP_5_LEFT_alt1 | ||
| CTGGATCGAGTGAACAGGCAG | ||
| >H1pdmMP_6_LEFT | ||
| AAGCGAATGGGAGTGCAGATG | ||
| >H1pdmMP_6_LEFT_alt1 | ||
| GCGGATGGGAGTGCAGATG | ||
| >H1pdmMP_last_LEFT | ||
| TCATTGGGATCTTGCACCTGA |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,130 @@ | ||
| >H3N2HA_0_LEFT | ||
| CAGCAAAAGCAGGGGATAATTCT | ||
| >H3N2HA_1_LEFT | ||
| CACCATGCAGTACCAAACGGAA | ||
| >H3N2HA_2_LEFT_me | ||
| TGCGACAGTCCTCATCAGATC | ||
| >H3N2HA_2_LEFT_me_alt1 | ||
| AATATGCAACAGTCCTCATCAGATC | ||
| >H3N2HA_3_LEFT | ||
| ATGATGTGCCGGATTATGCCTC | ||
| >H3N2HA_3_LEFT_alt1 | ||
| ATGATGTGCCGGATTATGCATC | ||
| >H3N2HA_4_LEFT | ||
| GGAGTCACTCAAAACGGAACAAG | ||
| >H3N2HA_4_LEFT_alt1 | ||
| TGGAGTCACTCAAAACGGAAAAAG | ||
| >H3N2HA_4_LEFT_alt2 | ||
| TGGAGTCAAACAAAACGGAACAAG | ||
| >H3N2HA_4.5_LEFT_new2_alt1 | ||
| GTGACTATGCCAAACAAGGAACA | ||
| >H3N2HA_4.5_LEFT_new2_alt2 | ||
| CGTGACTATGCCAAACAATGAACA | ||
| >H3N2HA_5_LEFT | ||
| TCAGGAAGAATCACAGTATCTACCAA | ||
| >H3N2HA_5_LEFT_alt1 | ||
| TCAGGAAGAATCACAGTCTCTACCAA | ||
| >H3N2HA_5_LEFT_alt2 | ||
| TCAGGAAGAATCACAGTATCTACCAG | ||
| >H3N2HA_6_LEFT | ||
| GGAATCTGATTGCTCCTAGGGG | ||
| >H3N2HA_6_LEFT_alt1 | ||
| GGGAATCTAATTGCTCCTAGGGG | ||
| >H3N2HA_7_LEFT | ||
| AACAGGATCACATACGGGGC | ||
| >H3N2HA_7_LEFT_alt1 | ||
| GTAAACAGGATCACATATGGGGC | ||
| >H3N2HA_8_LEFT | ||
| GTTGGTACGGTTTCAGGCATCA | ||
| >H3N2HA_8_LEFT_alt1 | ||
| GGTACGGCTTCAGGCATCA | ||
| >H3N2HA_8_LEFT_alt2 | ||
| GTTGGTACGGCTTCAGACATCA | ||
| >H3N2HA_9_LEFT_new2 | ||
| CCAACGAGAAATTCCATCAGATTGA | ||
| >H3N2HA_10_LEFT | ||
| TTGATCTAACTGACTCAGAAATGAACAA | ||
| >H3N2HA_10_LEFT_alt1 | ||
| TTGACCTAACTGACTCAGAAATGAACAA | ||
| >H3N2HA_last_LEFT_new3_alt1 | ||
| CAACCGGTTCCAGATCAAGGG | ||
| >H3N2HA_last_LEFT_new3_alt2 | ||
| CAACCGGTTCCAGATCAAAGG | ||
| >H3N2NA_0_LEFT | ||
| AGCAAAAGCAGGAGTAAAGATGAA | ||
| >H3N2NA_2_LEFT_new1_alt1 | ||
| CCCCCAAACAACCAAGTGATG | ||
| >H3N2NA_2_LEFT_new1_alt2 | ||
| CCCCCCAAATAACCAAGTGATG | ||
| >H3N2NA_2_LEFT_new1_alt3 | ||
| CCCCCGAATAACCAAGTGATG | ||
| >H3N2NA_3_LEFT | ||
| TGTGACATTACAGGATTTGCACC | ||
| >H3N2NA_3_LEFT_alt1 | ||
| GTGGCATTACAGGATTTGCACC | ||
| >H3N2NA_4_LEFT_new_alt1 | ||
| CGTGCATTCAAATAACACAGTACGT | ||
| >H3N2NA_4_LEFT_new_alt2 | ||
| TGCATTCAAATAACACAGCACGT | ||
| >H3N2NA_5_LEFT | ||
| CACGATGGAAAAGCATGGCTG | ||
| >H3N2NA_6_LEFT | ||
| CTCAGGACCCAGGAGTCAGAAT | ||
| >H3N2NA_6_LEFT_alt1 | ||
| CTCAGGACCCAGGAATCAGAAT | ||
| >H3N2NA_6_LEFT_alt2 | ||
| CTCAGAACCCAGGAGTCAGAAT | ||
| >H3N2NA_7_LEFT_me | ||
| GAGTGCTCTTGCTATCCTCGA | ||
| >H3N2NA_7_LEFT_me_alt1 | ||
| GAGTGCTCCTGCTATCCTCGA | ||
| >H3N2NA_8_LEFT_new1_alt1 | ||
| GATCCTAACAATGAAGAAGGTGGTC | ||
| >H3N2NA_8_LEFT_new1_alt2 | ||
| AACCCTAACAATGAAAAAGGTGGTC | ||
| >H3N2NA_8_LEFT_new1_alt3 | ||
| AATCCTAACAATGAAGAAGGTGGTC | ||
| >H3N2NA_8_LEFT_new1_alt4 | ||
| TGAACCCTAACAATGAAAAAGGTGATC | ||
| >H3N2NA_9_LEFT | ||
| GAAGGCTGGTCCAACCCTAA | ||
| >H3N2NA_9_LEFT_alt1 | ||
| TTGAAGGCTGGTCCAACTCTAA | ||
| >H3N2NA_9_LEFT_alt2 | ||
| AAGGCTGGTCCAACCCCAA | ||
| >H3N2NA_9_LEFT_alt3 | ||
| GAAGGCTGGTCCAATCCCAA | ||
| >H3N2NA_last_LEFT_new2 | ||
| GCTGCATCAATCGGTGCTTT | ||
| >A-M-UniF | ||
| GGGGGGAGCAAAAGCAGGTAG | ||
| >H3N2MP_re_2_LEFT_new1_alt1 | ||
| AGGCTCTCATGGAATGGCTAAAG | ||
| >H3N2MP_re_2_LEFT_new1_alt2 | ||
| AGGCTCTCATGGAATGGTTAAAG | ||
| >H3N2MP_3_LEFT | ||
| TCAAACTGTATAGGAAACTTAAGAGGGA | ||
| >H3N2MP_3_LEFT_alt1 | ||
| GTTAAACTGTATAGGAAACTTAAGAGGGA | ||
| >H3N2MP_3_LEFT_alt2 | ||
| AGTTAAACTGTATAGGAAACTTAAGAGAGA | ||
| >H3N2MP_4_LEFT | ||
| GGGGCTGTAACCACTGAAGT | ||
| >H3N2MP_5_LEFT | ||
| TGGATCAAGTGAGCAGGCAG | ||
| >H3N2MP_5_LEFT_alt1 | ||
| CTGGATCAAGTGAGCAAGCAG | ||
| >H3N2MP_5_LEFT_alt2 | ||
| CTGGATCAAGTGAACAGGCAG | ||
| >H3N2MP_6_LEFT | ||
| TTGCAGACCTATCAGAAACGAATG | ||
| >H3N2MP_6_LEFT_alt1 | ||
| GAAAATTTACAGACCTATCAGAAACGAATG | ||
| >H3N2MP_re_last_LEFT_new1 | ||
| ATTGGGATCTTGCACTTGATATTGT | ||
| >PrefixNX_1 | ||
| AGATGTGTATAAGAGACAG | ||
| >Trans1 | ||
| TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG | ||
| >Trans2 | ||
| GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,98 @@ | ||
| >H1pdmHA_0_RIGHT | ||
| GGCTACCCCTCTTAGTTTGCA | ||
| >H1pdmHA_0_RIGHT_alt1 | ||
| GGGCTACTCCTCTTAGTTTGCA | ||
| >H1pdmHA_1_RIGHT_me | ||
| GATTTCCCAGGATCCAGCCA | ||
| >H1pdmHA_2_RIGHT | ||
| ACCTTTCAAATGATGACACTGAGC | ||
| >H1pdmHA_3_RIGHT | ||
| TGAGCTTTGGGTATGAATTTCCTTT | ||
| >H1pdmHA_3_RIGHT_alt1 | ||
| TGAGCTTTGGGTATGAATTCCCTTT | ||
| >H1pdmHA_3_RIGHT_alt2 | ||
| GGTTGATCTTTGGGTATGATTTTCCTTT | ||
| >H1pdmHA_4_RIGHT | ||
| TGCTGTATCTTGATGACCCCAC | ||
| >H1pdmHA_4_RIGHT_alt1 | ||
| TGCTGTATCTTGATGTCCCCAC | ||
| >H1pdmHA_5_RIGHT | ||
| TCCAGTTGCTTCGAATGTTATTTTGT | ||
| >H1pdmHA_6_RIGHT_new_alt1 | ||
| TGAAATGGGAGGCTGGTGTT | ||
| >H1pdmHA_6_RIGHT_new_alt2 | ||
| TTCTGAAATGGGAGACTGGTGTT | ||
| >H1pdmHA_6_RIGHT_new_alt3 | ||
| TTCTGAAATGGAAGGCTGGTGTT | ||
| >H1pdmHA_7_RIGHT | ||
| ACCATCCATCTACCATCCCTGT | ||
| >H1pdmHA_7_RIGHT_alt1 | ||
| GTACCATCCATCTACCATTCCTGT | ||
| >H1pdmHA_8_RIGHT | ||
| GGTGGTTGAACTCTTTACCCAC | ||
| >H1pdmHA_8_RIGHT_alt1 | ||
| AAGGTGGTTGAACTCTTTACCAAC | ||
| >H1pdmHA_9_RIGHT | ||
| CTTCACATTTGAATCGTGATAGTCCA | ||
| >H1pdmHA_9_RIGHT_alt1 | ||
| TTCACATTTGAATCGTGGTAGTCCA | ||
| >H1pdmHA_10_RIGHT | ||
| TGAGTATTTTGGGTAGTCATAAGTCCC | ||
| >H1pdmHA_11_RIGHT | ||
| CACATCCAGAAACTGATTGCCC | ||
| >H1pdmHA_11_RIGHT_alt1 | ||
| ACATCCAGAAGCTGATTGCCC | ||
| >A-HA-R-new | ||
| CGGGTTATTAGTAGAAACAAGGGTG | ||
| >H1pdmNA_0_RIGHT | ||
| ACATATGTCTGATTTACCCAAGTATTGTT | ||
| >H1pdmNA_0_RIGHT_alt1 | ||
| ATGTCTGATTTACCCAAGTGTTGTT | ||
| >H1pdmNA_2_RIGHT | ||
| TGGTTCCCTTATGACAAACACATC | ||
| >H1pdmNA_3_RIGHT | ||
| TTGTATGGAGAGGGAACTTCACC | ||
| >H1pdmNA_4_RIGHT_me | ||
| CACATTCAGACTCTTGTGTTCTCAA | ||
| >H1pdmNA_5_RIGHT | ||
| CACTAGAATCAGGATAACAGGAGCA | ||
| >H1pdmNA_5_RIGHT_alt1 | ||
| ACTAGAATCAGGGTAACAGGAGCA | ||
| >H1pdmNA_5_RIGHT_alt2 | ||
| CTAGAGTCGGGATAACAGGAGCA | ||
| >H1pdmNA_6_RIGHT | ||
| CATTAGGGCGTGGATTGTCTCC | ||
| >H1pdmNA_7_RIGHT | ||
| TCCCAAATCATCTCAAAACCTTTTCT | ||
| >H1pdmNA_7_RIGHT_alt1 | ||
| TCCCAAATCATCTCAAAACCTTTCCT | ||
| >H1pdmNA_7_RIGHT_alt2 | ||
| TCCCAAATCATTTCAAAACCTTTTCT | ||
| >H1pdmNA_8_RIGHT_new1 | ||
| TCAACCCAGAAGCAAGGTCTTAT | ||
| >H1pdmNA_last_RIGHT | ||
| TTAGTAGAAACAAGGAGTTTTTTGAAC | ||
| >H1pdmMP_0_RIGHT | ||
| GGTGAGCGTGAACACAAATCC | ||
| >H1pdmMP_1_RIGHT | ||
| TTGGCCCCATGGAACGTTATTT | ||
| >H1pdmMP_1_RIGHT_alt1 | ||
| CTTGGCCCCATGGAATGTTATTT | ||
| >H1pdmMP_2_RIGHT_me | ||
| TATATGAGGCCCATGCAACTGG | ||
| >H1pdmMP_2_RIGHT_me_alt1 | ||
| TATATGAGGCCCATGCAACTTG | ||
| >H1pdmMP_3_RIGHT_me | ||
| ACCATTCTGTTCTCATGCCTGA | ||
| >H1pdmMP_3_RIGHT_me_alt1 | ||
| CACCATTCTGTTTTCATGCCTGA | ||
| >H1pdmMP_4_RIGHT_me | ||
| CAGCACTGGAGCTAGGATGAGT | ||
| >H1pdmMP_5_RIGHT_new1 | ||
| TCCCAATGATGTTTGCTGCAA | ||
| >H1pdmMP_6_RIGHT | ||
| CGTCAACATCCACAGCACTCT | ||
| >H1pdmMP_6_RIGHT_alt1 | ||
| ATCGTCAACATCTACAGCACTCT | ||
| >A-M-UniR | ||
| CCGGGTTATTAGTAGAAACAAGGTAG |
Oops, something went wrong.