Matt:LabNotes/2015-3-19: Difference between revisions
Jump to navigation
Jump to search
>Mzcai mNo edit summary |
>Mzcai mNo edit summary |
||
Line 25: | Line 25: | ||
samtools view -bS CA12kNov2014_V4cDNA_R1_H1H2.sam | samtools sort - CA12kNov2014_V4cDNA_R1_H1H2_sorted | samtools view -bS CA12kNov2014_V4cDNA_R1_H1H2.sam | samtools sort - CA12kNov2014_V4cDNA_R1_H1H2_sorted | ||
samtools view -h -F 4 CA12kNov2014_V4cDNA_R1_H1H2_sorted.bam > CA12kNov2014_V4cDNA_R1_H1H2_sorted_filtered.sam | samtools view -h -F 4 CA12kNov2014_V4cDNA_R1_H1H2_sorted.bam > CA12kNov2014_V4cDNA_R1_H1H2_sorted_filtered.sam | ||
CountReadsPer_Gene_Probe.pl | |||
*Verified with grep -c 'Gene' CA12kNov2014_V4gDNA_R1_H1H2_sorted_filtered.sam and grep -c 'Probe' CA12kNov2014_V4gDNA_R1_H1H2_sorted_filtered.sam | |||
**Differences in counts are accounted for by strings in header lines | |||
===Compare with Blue's BA8 bulk RNA-seq Gene Counts=== | |||
*/media/LTS_33T/BL_LTS33T/hNuc/Rizi_Bulk_Controls | |||
**RL-BA8-sec9-t-N701-15May14_S1/Counts_Gene (bulk tissue) | |||
**RL-BA8-sec9-n-N702-15May14_S2/Counts_Gene (bulk sorted neuronal nuclei) |
Revision as of 18:22, 20 March 2015
CA12k_Nov2014_V4 in vitro Capture Sequencing Analysis
CA12kNov2014_Probelist2Fasta.pl
bowtie2-build CA12k_Nov2014_V4_H1H2.fa CA12k_Nov2014_V4_H1H2
bowtie2 --phred33 -x CA12k_Nov2014_V4_H1H2 -q MC-20150121_CA12kNov2014_V4gDNA-1.R1.fastq > CA12kNov2014_V4gDNA_R1_H1H2.sam 2> CA12kNov2014_V4gDNA_stderr.txt &
2573875 reads; of these: 2573875 (100.00%) were unpaired; of these: 115745 (4.50%) aligned 0 times 2458058 (95.50%) aligned exactly 1 time 72 (0.00%) aligned >1 times 95.50% overall alignment rate
bowtie2 --phred33 -x CA12k_Nov2014_V4_H1H2 -q MC-20150121_CA12kNov2014_V4cDNA-2.R1.fastq > CA12kNov2014_V4cDNA_R1_H1H2.sam 2> CA12kNov2014_V4cDNA_stderr.txt &
2425688 reads; of these: 2425688 (100.00%) were unpaired; of these: 110744 (4.57%) aligned 0 times 2314903 (95.43%) aligned exactly 1 time 41 (0.00%) aligned >1 times 95.43% overall alignment rate
samtools view -bS CA12kNov2014_V4gDNA_R1_H1H2.sam | samtools sort - CA12kNov2014_V4gDNA_R1_H1H2_sorted samtools view -h -F 4 CA12kNov2014_V4gDNA_R1_H1H2_sorted.bam > CA12kNov2014_V4gDNA_R1_H1H2_sorted_filtered.sam
samtools view -bS CA12kNov2014_V4cDNA_R1_H1H2.sam | samtools sort - CA12kNov2014_V4cDNA_R1_H1H2_sorted samtools view -h -F 4 CA12kNov2014_V4cDNA_R1_H1H2_sorted.bam > CA12kNov2014_V4cDNA_R1_H1H2_sorted_filtered.sam
CountReadsPer_Gene_Probe.pl
- Verified with grep -c 'Gene' CA12kNov2014_V4gDNA_R1_H1H2_sorted_filtered.sam and grep -c 'Probe' CA12kNov2014_V4gDNA_R1_H1H2_sorted_filtered.sam
- Differences in counts are accounted for by strings in header lines
Compare with Blue's BA8 bulk RNA-seq Gene Counts
- /media/LTS_33T/BL_LTS33T/hNuc/Rizi_Bulk_Controls
- RL-BA8-sec9-t-N701-15May14_S1/Counts_Gene (bulk tissue)
- RL-BA8-sec9-n-N702-15May14_S2/Counts_Gene (bulk sorted neuronal nuclei)