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  • *I did the mapping using the script /home/kunzhang/bin/fastq2bamHg19.pl (should have used fastq2bam.pl because Idiographica do /home/kunzhang/softwares/samtools-0.1.12a/samtools pileup -c -f /home/kunzhang/HsGenome/hg19/hg19 Indx74.bowtie.sorted.bam > Indx74.pileup &
    2 KB (365 words) - 00:13, 13 November 2011
  • cat /home/kunzhang/seqStore/130120_HL141/s_1_1_Indx02.txt /home/kunzhang/seqStore/130120_HL141/s_5_1_Indx02.txt | trimFastq.pl 10 27 > Indx02_trimme cat /home/kunzhang/seqStore/130120_HL141/s_1_1_Indx05.txt /home/kunzhang/seqStore/130120_HL141/s_5_1_Indx05.txt | trimFastq.pl 10 27 > Indx05_trimme
    5 KB (636 words) - 18:08, 27 January 2013
  • *Run the following command in /home/kunzhang/seqStore/121226_HL140.2: 38.1 million of 40.2 million quality-filtered read *In the /home/kunzhang/RNAseq/Data/121226_HL140.2/RL_HBR directory, create eight folders for the e
    3 KB (447 words) - 03:12, 2 January 2013
  • ~/data_Syn_15T/HL163/BWA$ /home/kunzhang/softwares/samtools-latest/samtools view -b -f 4 s_10_1_Indx49_sorted.bam > ~/data_Syn_15T/HL163/BWA$ /home/kunzhang/softwares/samtools-latest/samtools view -h s_10_1_Indx49_sorted_unmapped.ba
    592 bytes (88 words) - 00:56, 26 February 2015
  • /home/kunzhang/softwares/samtools-latest/samtools flagstat PGP1_A1_ch01.sorted.bam > PGP1_ /home/kunzhang/softwares/samtools-latest/samtools flagstat PGP1_A1_ch02.sorted.bam > PGP1_
    19 KB (2,441 words) - 22:15, 30 June 2016
  • /Users/kunzhang/Downloads/samtools/misc/maq2sam-long ../MaqTarget/all.map > all.sam /Users/kunzhang/Downloads/samtools/samtools import /Users/kunzhang/WorkSpace/Exome/targets/ccdsExon_unique_miRNA_200bp.fa.combined.fai all.sam
    3 KB (452 words) - 23:19, 15 July 2009
  • nohup /home/kunzhang/softwares/tophat-latest/tophat -p 4 --solexa1.3-quals -o 1741_tophat -G / nohup /home/kunzhang/softwares/tophat-latest/tophat -p 4 --solexa1.3-quals -o 1818_tophat -G /
    4 KB (488 words) - 23:08, 7 October 2011
  • * Sequencing data is in genome-miner:'''/home/kunzhang/FreshReads/111209_SN1001''' ....txt /home/kunzhang/FreshReads/111209_SN1001/s_4_2_Indx4.txt | /home/kunzhang/bin/trimFastq.pl 27 83 >./HL111_GK0091-003<br>
    23 KB (3,080 words) - 17:19, 1 September 2012
  • /home/kunzhang/CpgMIP/MONOD/Data/WGBS_data/mld_block_hapInfo_July2015/All_chromosomes_comb /home/kunzhang/CpgMIP/MONOD/Data/1407-combined_RRBS/mld_blocks_hapInfo_July2015
    2 KB (264 words) - 17:35, 20 October 2015
  • *Build index: /home/kunzhang/softwares/Novocraft/novocraft/novoindex [options] [indexfile] [sequencefile *Align: /home/kunzhang/softwares/Novocraft/novocraft/novoalign [options]
    3 KB (417 words) - 00:55, 27 August 2013
  • nohup /home/kunzhang/softwares/cufflinks-1.1.0.Linux_x86_64/cufflinks -G /GenomeDB/UCSC/Mus_musc nohup /home/kunzhang/softwares/cufflinks-1.1.0.Linux_x86_64/cufflinks -G /GenomeDB/UCSC/Mus_musc
    2 KB (229 words) - 01:56, 22 November 2011
  • ...ad2 (PE 100 read, trimmed 27 bp from 5' end) were already stored in: /home/kunzhang/SeqStore/PennAfrican_Apr2011/Deconvoluted_reads less /home/kunzhang/SeqStore/PennAfrican_Apr2011/Deconvoluted_reads/PennAfrican_Batch1_Indx1_*
    9 KB (1,200 words) - 01:52, 19 February 2012
  • nohup /home/kunzhang/softwares/samtools-latest/samtools.pl pileup2fq PGP1_21_ch24.sorted.fragmen
    209 bytes (30 words) - 19:25, 26 February 2016
  • /home/kunzhang/softwares/bedtools-2.17.0/bin/bedtools subtract -a blood.UMRs.tab.txt -b h ...etitive.bed whole_blood_LMS_clusters_BED.txt | sort -k 1,1 -k 2,2n | /home/kunzhang/softwares/bedtools-2.17.0/bin/bedtools merge -d 80 -i - > blood.UMRs.non-r
    1 KB (199 words) - 21:42, 27 August 2014
  • /home/kunzhang/genomeSeq/Data/RL_iPSCs_full_data/multi_GATK_calls/Feb2013_vcf java -Xmx2g -jar /home/kunzhang/softwares/GenomeAnalysisTK-latest/GenomeAnalysisTK.jar
    2 KB (331 words) - 00:28, 28 January 2014
  • less /home/kunzhang/SeqStore/110902_HL101/s_1_Indx1.txt.gz /home/kunzhang/SeqStore/110902_HL101/s_2_Indx1.txt.gz > s12_Indx1.fq less /home/kunzhang/SeqStore/110902_HL101/s_1_Indx2.txt.gz /home/kunzhang/SeqStore/110902_HL101/s_2_Indx2.txt.gz > s12_Indx2.fq
    6 KB (919 words) - 17:59, 10 September 2011
  • ** /home/kunzhang/Exome/Solexa/090805_HL003 ** /home/kunzhang/Exome/scripts/variantCallerSoapSam.pl - calls consensus sequence using SOAP
    1 KB (179 words) - 21:24, 12 August 2009
  • ...2013|04242013]]||||hNPC lo/hi Pool||R04||RnaseIII||HL152||Lanes 6-8||/home/kunzhang/seqStore/130521_HL152|| ...013]]||||UHRR||RL.IVT.N6/N9||RNaseIII||HL155||Lanes 1,2 (id1,2,4,5)||/home/kunzhang/seqStore/130627_HiSeq_RapidRun/BL-UHRR-IVT-May28||
    10 KB (1,286 words) - 00:43, 6 February 2014
  • /home/kunzhang/softwares/samtools-latest/samtools flagstat EC-GM20431-2C-Mar19-VI-30_S14_L /home/kunzhang/softwares/samtools-latest/samtools flagstat EC-PGP1num21CoRE-Feb25-29_S37_L
    1 KB (240 words) - 18:24, 28 April 2015
  • /home/kunzhang/softwares/Novocraft/novocraft/novoindex V6S1.ndx Probelist_V6S1.fa /home/kunzhang/softwares/Novocraft/novocraft/novoindex V4S1.ndx Probelist_V4S1.fa
    5 KB (704 words) - 01:23, 31 August 2013
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