Jason Stajich hyphaltip
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| >MparAD039|ctg_19.g411.t1 | |
| MDGGLVLNFAAPTGDSAPTRLAKPKGGRWKDRVKVVKSVKRRIEVAGRPQSYSASTTPSE | |
| HSTAGPSTHSFAHDSSSLNDRSHSRSNNNDMDIDDYSYSEAAGGSKEAKMMHGKSQVQSS | |
| IFSPDTEIIPKVKTIHRPVGKPSNAPLNTSTFTGIGLDQDLAKHMEAKLRVTMPTTIQQK | |
| AIPVLLGPTRKVGDDIPKTDTDVIIQAETGSGKTLTYLLPIVNRLIESESSPALDLESKR | |
| SIGTLAIIMTPTRELAKQILQVLETLLSMPASSITGKKRSHWIVPGIVIGGDKKKSEKAR | |
| LRKGVNILVGTPGRLLDHLQNTKSFEVQSLRWLVLDEADRLLELGFEESMTAILKILDAR | |
| VKIAASVTSGNDTTKIWPQKRQTVLCSATLSDEVQRLAGTSLVDPIYISAKKEVANANGI | |
| PDSAVLAQEEKQVQQFSTPEQLKQLYVIAQAKLRLVTLTALLKSAFAGKDKNAKAPKMVV | |
| FLSSCDSVDFHHGLFSNAGKETKKEQTHDEYFGQSFENDNEDGDDDENKEDEIPDFVSAS |
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| >AJ878536 | |
| GGATCATTCATAAAAGGTGGTAGGTTGGTCTTGATAAAAAGGCCTTCTATCTACTTGACCTGTGCAATGTGGACTACATTCGATAGTTCT GAACTTGGAGATGGCAAATCCAGTAGGTCTTTTAAGGCTGAAATGGTGGCTCCAGAGGTACTTTTGGTACCAAAAATTTATATATACTAT TGTCAGATTTGATATACA | |
| GTGTCTGTTAGGACTTTTTGGCCTTCATTCACTATAAACTGTAGGATGGCTCTGTAGTGGGGTTCTGAATAC AAAAAACAACTTTTAGCAATGGATCTCTTGGTTTCCGCATCGATGAAGAGCGTAGCAAATTGCGATAATTAGTGCGAATTGCAGACCTTG CGAATCATCGAGTTCTTGAACGCATCTTGCACCTAG | |
| TAGTTTATTCTTCTAGGTACGGTTGCTTCAGTATTACGAAACTCAACAAGACCC AACTTTTGTGGTTTGGGACTTGGAGCTGGACTTGCTAGGGCCTCTTTGAGGGTCTTGGTAGTCTTAAATGGAGTATGCCAAAAGTCTTTT TGACCTTGTTTCAAAGAGATTGGACTATAAAAGTGGACCAAGGTCTGGTATGAT | |
| TTACCTTGGTTGTCCGATCTTTGGAGGTTAATGTGA TTGGGATTTTGGTTAGAGGTTTAGCCTCTAAAAAGATCTACCAAAACTGTAATCTGAAGCCAACCGAGACTACCCGCTGAACTTAA |
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| >JN206537.1 Radiomyces spectabilis strain CBS 255.60 28S ribosomal RNA gene, partial sequence | |
| GCGGAGGAAAAGAAACTAACAAGGATTCCCCTAGTAACGGCGAGTGAAGAGGGAAGAGCTCAAAGTTGGA | |
| ACCGAGTCGCTTTAAGTGATTTCGGGTTGTAAGCTAGAGAAGCGTTTTCCAGGCGAGCTGGGTATGTAAG | |
| TCCCTTGGAATAGGGCATCATAGAGGGTGAGAATCCCGTATGCCTACCCAAGCTAATATCGCCTTGTTGT | |
| GATACGCTTTCAAAGAGTCAGGTTGTTTGGGAATGCAGCCTAAAATGGGTGGTAAATCTCATCTAAAGCT | |
| AAATATTGGCGAGAGACCGATAGCGAACAAGTACCGTGAGGGAAAGATGAAAAGAACTTTGAAAAGAGAG | |
| TTAAACAGTATGTGAAATTGCTGAAAGGGAACCGTTTGAAGTTAGACTGGCTGGTCTATAATCAATCCTG | |
| GCTTTGGTTAGGATGCACTTGTAGGCCATTTTGCCTGCCAACGACAGTTTTTTGGGTAGGAAAAAAGTAC | |
| TGAGAAGGTAGCCTCGTTTTCGGATGAGGTGTTATAGCTCGGTACAAAATACTATCYGAGAGACTGAGGA | |
| ATGCAGCGAACGCTTATAGGCAGAGCTGCAGGTCGCTTGGTCAAATCTAGGCTGGAATTTCTTACCTCGG |
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| MUSCLE (3.8) multiple sequence alignment | |
| Uniq2;size=64653; ------------------------------------------------GTAGGTGAACCT | |
| Uniq165;size=1323; TACACGGCTTGGTCATTTAGAGGAAGTAAAAGTCGTAACAAGGTTTCCGTAGGTGAACCT | |
| ************ | |
| Uniq2;size=64653; GCGGAAGGATCATTACCTAGAGTTGTAGGCTTTGCCTGCTATCTCTTACCCATGTCTTTT | |
| Uniq165;size=1323; GCGGAAGGATCATTACCTAGAGTTGTAGGCTTTGCCTGCTATCTCTTACCCATGTCTTTT | |
| ************************************************************ |
hyphaltip
/ FLO1.ABH.FASTA.gz
Last active
October 26, 2016 09:16
FLO analysis of Nanopore Yeast assemblies
hyphaltip
/ FwdR1_split_library_log.txt
Last active
October 12, 2016 05:14
split_libraries results for FC534
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| # from /bigdata/stajichlab/shared/projects/Microbiome/data/2016-09_FC534/split_libraries_R1/split_library_log.txt | |
| Input file paths | |
| Mapping filepath: FC534_map.txt (md5: e759ae3c134cd9dc16dfeec94977fe59) | |
| Sequence read filepath: fastq/FC534_R1.fastq.gz (md5: 149e38bbfe266eb77137cb2aea6710aa) | |
| Barcode read filepath: fastq/FC534_I.fastq.gz (md5: 7e53d59e300a5ba15b1e70850515967d) | |
| Quality filter results | |
| Total number of input sequences: 11480826 | |
| Barcode not in mapping file: 218856 | |
| Read too short after quality truncation: 850839 |
hyphaltip
/ sexM-vs-NRRL1555genome.TFASTX
Created
October 12, 2016 04:59
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| # tfastx36 -E 1e-8 sexM.fa ../../ZyGoLife/datasets/genomes/DNA/Phycomyces_blakesleeanus_NRRL_1555.Phybl2.v2.fasta | |
| TFASTX compares a protein to a translated DNA data bank | |
| version 36.3.7a Jan, 2015(preload9) | |
| Please cite: | |
| Pearson et al, Genomics (1997) 46:24-36 | |
| Query: sexM.fa | |
| 1>>>tr|B0F2G8|B0F2G8_PHYBL Sex minus OS=Phycomyces blakesleeanus GN=sexM PE=4 SV=1 - 188 aa | |
| Library: ../../ZyGoLife/datasets/genomes/DNA/Phycomyces_blakesleeanus_NRRL_1555.Phybl2.v2.fasta | |
| 53939167 residues in 80 sequences |
hyphaltip
/ sexP-vs-Rstol.TFASTX
Last active
August 4, 2016 20:34
TFASTX sexP vs R.stol B9770 genome
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| # tfastx36 -E 1e-10 all_sexP.fa ../ref_genome/Rhizopus_stolonifer_B9770.fasta | |
| TFASTX compares a protein to a translated DNA data bank | |
| version 36.3.7a Jan, 2015(preload9) | |
| Please cite: | |
| Pearson et al, Genomics (1997) 46:24-36 | |
| Query: all_sexP.fa | |
| 1>>>tr|B0F2H1|B0F2H1_PHYBL Sex plus OS=Phycomyces blakesleeanus GN=sexP PE=4 SV=1 - 297 aa | |
| Library: ../ref_genome/Rhizopus_stolonifer_B9770.fasta | |
| 36816898 residues in 3703 sequences |
hyphaltip
/ JGI-Zoophthora_radicans_asmbl_info.txt
Created
May 16, 2016 18:58
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| Zoophthora radicans ATCC 208865/ARSEF 4784 | |
| Standard Draft | |
| Kurt LaButti, klabutti@lbl.gov | |
| 20140505 | |
| 1. Project Information | |
| est_gen_size_mb=500 | |
| final_deliv_proj_id=1015490 | |
| final_deliv_proj_name=Zoophthora radicans ATCC 208865/ARSEF 4784 Annotated Standard Draft |
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| mp <- read.table("/bigdata/wesslerlab/twrightsman/mercator_analysis/output/map") | |
| summary(mp) | |
| blocks = abs(mp$V3-mp$V4) # ref genome block sizes | |
| summary(blocks) | |
| pdf("block_dist.pdf") | |
| hist(blocks,100) |