EricChu:LabNotesMDA/2015-1-7: Difference between revisions

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* command: nohup ../../batch_bwa_fastq2bam.pl hg19 > EC_GMDev9Oct10_BWA_batch_fastq2bam.log &
* command: nohup ../../batch_bwa_fastq2bam.pl hg19 > EC_GMDev9Oct10_BWA_batch_fastq2bam.log &
* ../../get_covstats.pl > EC_GMDev9Oct10_BWA_covstat.txt &
* ../../get_covstats.pl > EC_GMDev9Oct10_BWA_covstat.txt &
* /home/kunzhang/softwares/samtools-0.1.19/samtools view -o s_1_1_Indx32_unique.sam s_1_1_Indx32_unique.bam

Revision as of 20:15, 8 January 2015

Mapping New Sequencing Libraries

  • These 9 single cell libraries were sequenced in HL175. GM stands for GM20431.
  1. GM Dev9 Oct10 (Index 9-16). Asked for 10 million reads. Sequenced in Lane 1.
  2. PGP1 Dev7 Oct6 (Index 17-24). Asked for 10 million reads. Sequenced in Lane 1.
  3. GM Dev9.2 Oct23 (Index 25-32). Asked for 20 million reads. Sequenced in Lane 1. GM Dev9.2 Oct23 (Index 9-24). Asked for 40 million reads. Sequenced in Lane 2.
  4. GM Dev9.2 Nov4 (Index9-32). Asked for 40 million reads. Sequenced in Lane3.
  5. GM Dev9 Nov14 (Index9-32). Asked for 40 million reads. Sequenced in Lane4.
  6. GM Dev9 Nov18 (Index9-32). Asked for 40 million reads. Sequenced in Lane5.
  7. GM Dev9 Dec2 (Index9-32). Asked for 40 million reads. Sequenced in Lane6.
  8. GM Dev9 Dec3 (Index9-32). Asked for 40 million reads. Sequenced in Lane7.
  9. GM Dev7 Dec9 (Index9-32). Asked for 40 million reads. Sequenced in Lane8.

Commands

  • reference: http://genome-tech.ucsd.edu/LabNotes/index.php/EricChu:LabNotesMDA/2014-8-25
  • txt files were copied to /data_Syn_15T/HL175/
  • Each single cell data have its own folder.
  • For example, in /data_Syn_15T/HL175/GMDev9Oct10
  • command: nohup ../../batch_bwa_fastq2bam.pl hg19 > EC_GMDev9Oct10_BWA_batch_fastq2bam.log &
  • ../../get_covstats.pl > EC_GMDev9Oct10_BWA_covstat.txt &
  • /home/kunzhang/softwares/samtools-0.1.19/samtools view -o s_1_1_Indx32_unique.sam s_1_1_Indx32_unique.bam