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https://github.com/fjruizruano/ngs-protocols
05 April 2024, 22:19:15 UTC
Revision 09d12f8d08a94a91a3e992a50c5791ae72070afe authored by Paquillo on 11 February 2021, 22:58:53 UTC, committed by Paquillo on 11 February 2021, 22:58:53 UTC 
adding rm_getseq_stats.py
1 parent a948c24
History
Tip revision: 09d12f8d08a94a91a3e992a50c5791ae72070afe authored by Paquillo on 11 February 2021, 22:58:53 UTC
adding rm_getseq_stats.py
Tip revision: 09d12f8
File Mode Size
FastA.split.pl -rwxr-xr-x 1.1 KB
FastQ.split.pl -rwxr-xr-x 1.1 KB
LICENSE -rw-r--r-- 34.3 KB
README.md -rw-r--r-- 9.6 KB
SE_deconseq_run.py -rwxr-xr-x 3.0 KB
SE_rexp_prepare.py -rwxr-xr-x 2.7 KB
alignment_copy_paste.py -rwxr-xr-x 722 bytes
annot_to_rexp.py -rwxr-xr-x 854 bytes
bam_consensus.py -rwxr-xr-x 1.2 KB
bam_coverage_join.py -rwxr-xr-x 1.3 KB
bam_var_join.py -rwxr-xr-x 1.3 KB
bg_count.py -rwxr-xr-x 764 bytes
blat_recursive.py -rwxr-xr-x 1.5 KB
blat_recursive_hard.py -rwxr-xr-x 1.4 KB
bowtie2_protocol.py -rwxr-xr-x 1.6 KB
bowtie2_recursive.py -rwxr-xr-x 1.5 KB
bwa_mem_protocol.py -rwxr-xr-x 1.4 KB
bwa_protocol.py -rwxr-xr-x 1.6 KB
cd_hit_count_clusters.py -rwxr-xr-x 1.6 KB
cd_hit_filter_size.py -rwxr-xr-x 1.6 KB
count_acgtn.py -rwxr-xr-x 685 bytes
count_bases_fastq.py -rwxr-xr-x 1.1 KB
count_kmer.py -rwxr-xr-x 591 bytes
count_reads_bam.py -rwxr-xr-x 738 bytes
coverage_graphics.py -rwxr-xr-x 13.3 KB
coverage_graphics_coord.py -rwxr-xr-x 8.8 KB
coverage_seq_bed.py -rwxr-xr-x 1.1 KB
coverage_window.py -rwxr-xr-x 1.5 KB
cut_seq_unequal.py -rwxr-xr-x 370 bytes
deconseq_run.py -rwxr-xr-x 3.8 KB
dimerator.py -rwxr-xr-x 658 bytes
divnuc_bam.py -rwxr-xr-x 3.3 KB
divnuc_plot.py -rwxr-xr-x 795 bytes
divsum_ab.py -rwxr-xr-x 3.4 KB
divsum_analysis.py -rwxr-xr-x 974 bytes
divsum_count.py -rwxr-xr-x 1.0 KB
divsum_join_annot.py -rwxr-xr-x 1.2 KB
divsum_stats.py -rwxr-xr-x 3.0 KB
divsum_to_rl.py -rwxr-xr-x 8.7 KB
dnapipete_createdb.py -rwxr-xr-x 980 bytes
ecopcr_db.py -rwxr-xr-x 824 bytes
extract_barcoded_reads_from_bam.py -rwxr-xr-x 1.9 KB
extract_member_reads_rexp.py -rwxr-xr-x 1.0 KB
extract_no_seq.py -rwxr-xr-x 906 bytes
extract_reads_blat.py -rwxr-xr-x 356 bytes
extract_reads_rm.py -rwxr-xr-x 503 bytes
extract_regions_bam.py -rwxr-xr-x 873 bytes
extract_seq.py -rwxr-xr-x 857 bytes
extract_seq_bam.py -rwxr-xr-x 1.3 KB
extract_seq_len.py -rwxr-xr-x 839 bytes
extract_seq_regions.py -rwxr-xr-x 1.1 KB
fasta_filter_by_length.py -rwxr-xr-x 1.1 KB
fasta_sequence_len.py -rwxr-xr-x 335 bytes
fastq-combine-pe.py -rwxr-xr-x 3.8 KB
fastq-pe-random.py -rwxr-xr-x 1.4 KB
fastq_edit_ids.py -rwxr-xr-x 2.3 KB
fastq_edit_ids_sra.py -rwxr-xr-x 1.9 KB
fastq_paired_combine_id.py -rwxr-xr-x 1.3 KB
find_exclusive_kmers.py -rwxr-xr-x 1.3 KB
gatk_protocol.py -rwxr-xr-x 2.9 KB
get_no_blat.py -rwxr-xr-x 559 bytes
get_var_library.py -rwxr-xr-x 658 bytes
gff_creator.py -rwxr-xr-x 305 bytes
id_rmasker.py -rwxr-xr-x 296 bytes
id_rmasker_rexp.py -rwxr-xr-x 384 bytes
join_multiple_lists.py -rwxr-xr-x 734 bytes
join_multiple_lists_var.py -rwxr-xr-x 827 bytes
join_rm_list.py -rwxr-xr-x 745 bytes
kimura_window.py -rwxr-xr-x 2.1 KB
kmer_to_fasta.py -rwxr-xr-x 219 bytes
longranger_prepare_reference.py -rwxr-xr-x 1.0 KB
mapping_blat_gs.py -rwxr-xr-x 5.4 KB
mapping_blat_gs_hard.py -rwxr-xr-x 5.4 KB
mapping_blat_gs_light.py -rwxr-xr-x 5.7 KB
mapping_blat_gs_saver.py -rwxr-xr-x 9.9 KB
mapping_blat_gs_single_end.py -rwxr-xr-x 2.8 KB
massive_phylogenies_figure.py -rwxr-xr-x 1021 bytes
massive_phylogeny.py -rwxr-xr-x 1.7 KB
massive_phylogeny_raxml_support.py -rwxr-xr-x 1.4 KB
mitobim_run.py -rwxr-xr-x 3.6 KB
mreps_extract.py -rwxr-xr-x 1.0 KB
peru_protocol.py -rwxr-xr-x 1.9 KB
raxml_protocol.py -rwxr-xr-x 1.6 KB
reduce_bam.py -rwxr-xr-x 1022 bytes
remove_ns.py -rwxr-xr-x 392 bytes
repeat_landscape_decimal.py -rwxr-xr-x 1.6 KB
repeat_landscape_decimal_050.py -rwxr-xr-x 1.7 KB
repeat_masker_run.py -rwxr-xr-x 328 bytes
repeat_masker_run_big.py -rwxr-xr-x 1.6 KB
repeat_masker_run_big_microsat.py -rwxr-xr-x 1.4 KB
replace_patterns.py -rwxr-xr-x 574 bytes
rexp_annot.py -rwxr-xr-x 1.0 KB
rexp_get_contigs.py -rwxr-xr-x 1.1 KB
rexp_get_contigs_re2.py -rwxr-xr-x 1.1 KB
rexp_prepare.py -rwxr-xr-x 3.7 KB
rexp_prepare_deconseq.py -rwxr-xr-x 3.1 KB
rexp_prepare_normaltag.py -rwxr-xr-x 3.7 KB
rexp_select_contigs.py -rwxr-xr-x 870 bytes
rm_clas_seq.py -rwxr-xr-x 1.1 KB
rm_clas_seq_names.py -rwxr-xr-x 2.1 KB
rm_cluster_external.py -rwxr-xr-x 6.0 KB
rm_count_matches.py -rwxr-xr-x 935 bytes
rm_count_matches_monomers.py -rwxr-xr-x 1.2 KB
rm_getseq.py -rwxr-xr-x 1.4 KB
rm_getseq_annot.py -rwxr-xr-x 1.4 KB
rm_getseq_split.py -rwxr-xr-x 2.5 KB
rm_getseq_stats.py -rwxr-xr-x 1.8 KB
rm_homology.py -rwxr-xr-x 1.5 KB
rm_join_out.py -rwxr-xr-x 1.4 KB
rm_join_tbl.py -rwxr-xr-x 546 bytes
run_abyss.py -rwxr-xr-x 1.8 KB
sat_cross_libraries.py -rwxr-xr-x 1.1 KB
sat_cutter.py -rwxr-xr-x 1.5 KB
sat_subfam2fam.py -rwxr-xr-x 649 bytes
sat_subfam2fam_multi.py -rwxr-xr-x 1.3 KB
sat_subfam2fam_multi_support.py -rwxr-xr-x 565 bytes
satminer_quant.py -rwxr-xr-x 1.5 KB
search_issr_1nt.py -rwxr-xr-x 989 bytes
search_issr_2nt.py -rwxr-xr-x 989 bytes
sequence_ref_alt.py -rwxr-xr-x 1.1 KB
snp_calling_bchr.py -rwxr-xr-x 2.5 KB
snp_calling_bchr_z10.py -rwxr-xr-x 2.5 KB
snp_calling_dn_ds.py -rwxr-xr-x 1.3 KB
split_illumina.py -rwxr-xr-x 735 bytes
sra_download.py -rwxr-xr-x 452 bytes
ssaha2_run.py -rwxr-xr-x 2.2 KB
ssaha2_run_multi.py -rwxr-xr-x 4.2 KB
ssaha2_run_multi_pe_se.py -rwxr-xr-x 7.3 KB
ssaha2_run_multi_se.py -rwxr-xr-x 3.3 KB
stampy_protocol.py -rwxr-xr-x 1.1 KB
subsampler.py -rwxr-xr-x 1.2 KB
taxonomy_retrieve.py -rwxr-xr-x 784 bytes
trinity_extract_longest.py -rwxr-xr-x 864 bytes
trinity_extract_longest2.py -rwxr-xr-x 864 bytes
trinotate_auto.py -rwxr-xr-x 3.1 KB
trna_clustering.py -rwxr-xr-x 1.3 KB
unshuffle.py -rwxr-xr-x 669 bytes

README.md

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