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https://github.com/cyaguesa/SL-quant
05 April 2024, 20:04:02 UTC
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Revision Author Date Message Commit Date
76117b8 Carlo Yague 27 August 2019, 14:29:17 UTC Fix EOF warning sort issue in -sp mode Was aware of sort bug thanks to Yeonsu Jeon querry by email. 27 August 2019, 14:29:17 UTC
f61d12b Carlo Yague 26 September 2018, 15:38:36 UTC Set theme jekyll-theme-modernist 26 September 2018, 15:38:36 UTC
33e9fa9 Carlo Yague 26 September 2018, 12:57:13 UTC Set theme jekyll-theme-architect 26 September 2018, 12:57:13 UTC
93f376d Carlo Yague 21 August 2018, 13:33:15 UTC Fix for bug issue #1 https://github.com/cyaguesa/SL-quant/issues/1 21 August 2018, 13:33:15 UTC
0ea6a63 Carlo Yague 20 July 2018, 06:23:42 UTC link to manuscript added 20 July 2018, 06:23:42 UTC
e197d46 Carlo Yague 24 May 2018, 13:37:12 UTC reverted last change because bug 24 May 2018, 13:37:12 UTC
d3ff113 Carlo Yague 24 May 2018, 13:33:15 UTC generalized to other SL names for briggsae SL.fasta 24 May 2018, 13:33:15 UTC
4266b29 Carlo Yague 24 May 2018, 11:39:08 UTC more robust mkdir -p 24 May 2018, 11:39:08 UTC
f715bad Carlo Yague 18 April 2018, 07:51:24 UTC final update many changes 18 April 2018, 07:51:24 UTC
5dd681c Carlo Yague 16 April 2018, 08:48:54 UTC small update 16 April 2018, 08:48:54 UTC
aacf7c5 Carlo Yague 13 April 2018, 14:15:41 UTC update link again 13 April 2018, 14:15:41 UTC
2342068 Carlo Yague 13 April 2018, 14:14:37 UTC link update 13 April 2018, 14:14:37 UTC
9da25c4 Carlo Yague 13 April 2018, 13:24:42 UTC update of adaptation and consensus Identification of SL trans-spliced sites > consensus Adaptation to other species 13 April 2018, 13:24:42 UTC
d0267bf Carlo Yague 06 April 2018, 09:02:24 UTC added gene_anotation parameter for featurecounts 06 April 2018, 09:02:24 UTC
320accb Carlo Yague 06 April 2018, 08:55:00 UTC usage exemple corrected 06 April 2018, 08:55:00 UTC
32b021b Carlo Yague 06 April 2018, 08:54:19 UTC featurecounts read orientation corrected a bug with featurecounts read orientation 06 April 2018, 08:54:19 UTC
5e5e1cd Carlo Yague 05 April 2018, 15:00:03 UTC typo 05 April 2018, 15:00:03 UTC
6f9fec3 Carlo Yague 04 April 2018, 13:49:38 UTC integrate -s --sensitive datasets and more 04 April 2018, 13:49:38 UTC
d7cb90a Carlo Yague 04 April 2018, 12:33:13 UTC SL trans-spliced sites 04 April 2018, 12:33:13 UTC
31924bd Carlo Yague 04 April 2018, 12:31:59 UTC Update README.md 04 April 2018, 12:31:59 UTC
8fd7fdb Carlo Yague 04 April 2018, 12:29:29 UTC changed analysis 04 April 2018, 12:29:29 UTC
72fa86e Carlo Yague 04 April 2018, 12:17:15 UTC Create SL_sites.sh 04 April 2018, 12:17:15 UTC
089888a Carlo Yague 04 April 2018, 11:35:44 UTC random read fixed 1000003 -> 1000000 04 April 2018, 11:35:44 UTC
6468194 Carlo Yague 04 April 2018, 11:33:22 UTC remove rename chr 04 April 2018, 11:33:22 UTC
8a6a58e Carlo Yague 04 April 2018, 11:33:01 UTC Update chrom_summary.txt 04 April 2018, 11:33:01 UTC
ac4c9c5 Carlo Yague 04 April 2018, 11:30:59 UTC remove chr* 04 April 2018, 11:30:59 UTC
30d58b2 Carlo Yague 04 April 2018, 11:29:03 UTC remove bowtie requirements 04 April 2018, 11:29:03 UTC
e57ef97 Carlo Yague 04 April 2018, 09:14:46 UTC added trimmomatic installation instructions 04 April 2018, 09:14:46 UTC
43f9e2b Carlo Yague 04 April 2018, 08:49:05 UTC Update SL_cutadapt.sh 04 April 2018, 08:49:05 UTC
5126ee7 Carlo Yague 04 April 2018, 08:48:29 UTC Update SL-quant.sh 04 April 2018, 08:48:29 UTC
ab79e36 Carlo Yague 04 April 2018, 08:41:37 UTC Add files via upload 04 April 2018, 08:41:37 UTC
26e888d Carlo Yague 04 April 2018, 07:22:33 UTC typo 04 April 2018, 07:22:33 UTC
5d15499 Carlo Yague 04 April 2018, 07:12:33 UTC added perm change for SL-sites and SL-cutadapt 04 April 2018, 07:12:33 UTC
3f3d2b2 Carlo Yague 04 April 2018, 07:10:51 UTC Update set-up.sh 04 April 2018, 07:10:51 UTC
7485756 Carlo Yague 04 April 2018, 07:08:55 UTC Update set-up.sh 04 April 2018, 07:08:55 UTC
090946a Carlo Yague 04 April 2018, 07:07:31 UTC Update set-up.sh 04 April 2018, 07:07:31 UTC
32e0da7 Carlo Yague 04 April 2018, 07:06:55 UTC change to WS262 annotation for consistency 04 April 2018, 07:06:55 UTC
f446089 Carlo Yague 03 April 2018, 11:27:17 UTC -p -s order correction 03 April 2018, 11:27:17 UTC
8eb4f16 Carlo Yague 02 April 2018, 13:53:37 UTC bug correction affecting single-end sensitive mode: file name correction 02 April 2018, 13:53:37 UTC
f397a24 Carlo Yague 02 April 2018, 11:33:19 UTC update single-end dataset cmds 02 April 2018, 11:33:19 UTC
6f4ce54 Carlo Yague 02 April 2018, 11:31:52 UTC Update map_reads_modENCODE.sh 02 April 2018, 11:31:52 UTC
38473d0 Carlo Yague 02 April 2018, 11:28:35 UTC Update map_reads_modENCODE.sh 02 April 2018, 11:28:35 UTC
13df4c5 Carlo Yague 02 April 2018, 11:27:27 UTC update 02 April 2018, 11:27:27 UTC
d4eb043 Carlo Yague 02 April 2018, 10:19:29 UTC typo correction 02 April 2018, 10:19:29 UTC
0a2cd04 Carlo Yague 02 April 2018, 06:48:50 UTC Delete temp 02 April 2018, 06:48:50 UTC
0637501 Carlo Yague 02 April 2018, 06:20:51 UTC mkdir output 02 April 2018, 06:20:51 UTC
53ef6b3 Carlo Yague 01 April 2018, 15:44:55 UTC typo 01 April 2018, 15:44:55 UTC
4f8a481 Carlo Yague 16 March 2018, 12:14:10 UTC Add files via upload 16 March 2018, 12:14:10 UTC
3fd7633 Carlo Yague 16 March 2018, 12:13:44 UTC Delete test_unmapped.bam 16 March 2018, 12:13:44 UTC
8308aeb Carlo Yague 16 March 2018, 12:13:38 UTC Delete test_mapped.bam 16 March 2018, 12:13:38 UTC
81aac04 Carlo Yague 16 March 2018, 12:11:13 UTC typo correction 16 March 2018, 12:11:13 UTC
c4bd22c Carlo Yague 15 March 2018, 15:03:27 UTC Update README.md 15 March 2018, 15:03:27 UTC
c12722a Carlo Yague 15 March 2018, 15:02:38 UTC Update README.md 15 March 2018, 15:02:38 UTC
5606dc3 Carlo Yague 15 March 2018, 14:55:54 UTC updated usage 15 March 2018, 14:55:54 UTC
f75026d Carlo Yague 15 March 2018, 14:15:43 UTC Delete SL_cutadapt.sh improved and incorporated into SL-quant main function 15 March 2018, 14:15:43 UTC
24b7274 Carlo Yague 15 March 2018, 14:14:51 UTC Add files via upload 15 March 2018, 14:14:51 UTC
567932f Carlo Yague 15 March 2018, 14:14:27 UTC Create temp 15 March 2018, 14:14:27 UTC
1671f3b Carlo Yague 15 March 2018, 14:14:13 UTC Delete reads 15 March 2018, 14:14:13 UTC
aa454fd Carlo Yague 15 March 2018, 14:12:55 UTC temp 15 March 2018, 14:12:55 UTC
d9b91f2 Carlo Yague 15 March 2018, 14:12:21 UTC Delete test_unmapped.bam 15 March 2018, 14:12:21 UTC
aac9c38 Carlo Yague 15 March 2018, 14:12:13 UTC Delete test_mapped.bam 15 March 2018, 14:12:13 UTC
019fec5 Carlo Yague 15 March 2018, 14:11:40 UTC Update SL-quant.sh 15 March 2018, 14:11:40 UTC
0bd8d9f Carlo Yague 15 March 2018, 14:09:04 UTC picard function update SORT_ORDER=unsorted --> cause does not assume the same ordering 15 March 2018, 14:09:04 UTC
e0e5430 Carlo Yague 15 March 2018, 13:49:35 UTC add cool mkdir for dir/base mkdir -p "${3%/*}" 15 March 2018, 13:49:35 UTC
deafb34 Carlo Yague 15 March 2018, 13:39:46 UTC fix issue with bam2fastq conversion using bedtools instead of picard is easier 15 March 2018, 13:39:46 UTC
e857e73 Carlo Yague 15 March 2018, 13:13:55 UTC Add files via upload file for original 'cutadapt' method using both forward and reverse sequences 15 March 2018, 13:13:55 UTC
bee4707 Carlo Yague 15 March 2018, 12:20:24 UTC big update Add --sensitive option Add parsing of arguments Updated usage 15 March 2018, 12:20:24 UTC
fa5f2ee Carlo Yague 12 March 2018, 12:02:37 UTC typo correction 12 March 2018, 12:02:37 UTC
cff2628 Carlo Yague 12 March 2018, 12:01:20 UTC add send parameter 12 March 2018, 12:01:20 UTC
95faf3a Carlo Yague 12 March 2018, 11:47:14 UTC typo 12 March 2018, 11:47:14 UTC
d162cdc Carlo Yague 12 March 2018, 10:34:16 UTC another fix on R2 issue need intermediate file when using SL-quant in single-end mode with paired-end data 12 March 2018, 10:34:16 UTC
cfc20cb Carlo Yague 12 March 2018, 10:11:24 UTC fix issue with R2 reads need intermediate file with only R2 reads in single-end mode with paired-end data 12 March 2018, 10:11:24 UTC
148ef96 Carlo Yague 12 March 2018, 09:52:07 UTC signle-end mode with paired-end data only R2 reads are considered to avoid read ID conflicts 12 March 2018, 09:52:07 UTC
35b1b1d Carlo Yague 12 March 2018, 09:09:40 UTC more strandness update 12 March 2018, 09:09:40 UTC
1938225 Carlo Yague 12 March 2018, 09:05:40 UTC added support for blast strandness 12 March 2018, 09:05:40 UTC
0c1cb67 Carlo Yague 09 March 2018, 09:23:03 UTC Update SL.fasta 09 March 2018, 09:23:03 UTC
f517c37 Carlo Yague 09 March 2018, 07:15:21 UTC added filter on send==22 09 March 2018, 07:15:21 UTC
523b98c Carlo Yague 09 March 2018, 07:10:22 UTC added makeblastdb 09 March 2018, 07:10:22 UTC
3a04f4c Carlo Yague 09 March 2018, 07:09:12 UTC Delete SL.fasta.nsq moved db formation in set-up.sh 09 March 2018, 07:09:12 UTC
4a5fafb Carlo Yague 09 March 2018, 07:09:04 UTC Delete SL.fasta.nin moved db formation in set-up.sh 09 March 2018, 07:09:04 UTC
2125967 Carlo Yague 09 March 2018, 07:08:44 UTC Delete SL.fasta.nhr moved db formation in set up 09 March 2018, 07:08:44 UTC
92035ad Carlo Yague 09 March 2018, 07:04:17 UTC removed polyA and polyT and cropped all SL sequences to 22 nt 09 March 2018, 07:04:17 UTC
02b108a Carlo Yague 08 March 2018, 15:30:31 UTC replaced tophat2 by hisat2 08 March 2018, 15:30:31 UTC
424815e Carlo Yague 08 March 2018, 15:12:58 UTC Update SL-quant.sh 08 March 2018, 15:12:58 UTC
b2455b4 Carlo Yague 08 March 2018, 15:12:26 UTC correct featurecounts strand orientation 08 March 2018, 15:12:26 UTC
3f6eda6 Carlo Yague 08 March 2018, 14:27:37 UTC update usage 08 March 2018, 14:27:37 UTC
9fb30f6 Carlo Yague 08 March 2018, 14:12:50 UTC correct hisat2 call 08 March 2018, 14:12:50 UTC
f4feb6a Carlo Yague 08 March 2018, 13:34:59 UTC unmapped.sam processing added -un option to hisat + conversion SAM/BAM 08 March 2018, 13:34:59 UTC
e320a78 Carlo Yague 08 March 2018, 13:23:22 UTC update cutadapt version 08 March 2018, 13:23:22 UTC
5a5cb50 Carlo Yague 08 March 2018, 13:22:52 UTC update parameters 08 March 2018, 13:22:52 UTC
082ae5f Carlo Yague 08 March 2018, 13:21:07 UTC correct typo 08 March 2018, 13:21:07 UTC
e5434b1 Carlo Yague 08 March 2018, 13:19:02 UTC replaced bowtie2 by hisat2 08 March 2018, 13:19:02 UTC
245d17d Carlo Yague 08 March 2018, 13:03:13 UTC corrected typo in description 08 March 2018, 13:03:13 UTC
e7edc75 Carlo Yague 08 March 2018, 13:02:32 UTC Update map_reads_modENCODE.sh 08 March 2018, 13:02:32 UTC
85d6390 Carlo Yague 08 March 2018, 13:02:22 UTC replaced tophat2 by hisat2 08 March 2018, 13:02:22 UTC
a1f84d7 Carlo Yague 08 March 2018, 10:36:13 UTC Create SL_cutadapt.sh # Implementation of the SL-containing reads identification strategy used in (Tourasse et al., 2017) [doi:10.1101/gr.224626.117] 08 March 2018, 10:36:13 UTC
3424b2f Carlo Yague 08 March 2018, 10:35:29 UTC Update set-up.sh 08 March 2018, 10:35:29 UTC
abb0516 Carlo Yague 08 March 2018, 09:36:51 UTC added build hisat2 index 08 March 2018, 09:36:51 UTC
31d53aa Carlo Yague 27 February 2018, 14:20:07 UTC update return_pos_in_operon 27 February 2018, 14:20:07 UTC
5aa9230 Carlo Yague 19 February 2018, 14:22:13 UTC added 'Identification of trans-splice sites' 19 February 2018, 14:22:13 UTC
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