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Merge pull request #131 from joachimwolff/develop
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Added bam compression from old tutorial
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@bgruening
bgruening committed Oct 2, 2017
2 parents 45e8326 + f393a03 commit a7861f8
Showing 1 changed file with 22 additions and 22 deletions.
44 changes: 22 additions & 22 deletions docs/content/mES-HiC_analysis.rst
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Expand Up @@ -105,35 +105,35 @@ hisat2

.. code:: bash
hisat2 -x hisat2/mm10_index --threads 8 ../original_data/SRR1956527_1.fastq --reorder -S SRR1956527_1.sam
hisat2 -x hisat2/mm10_index --threads 8 ../original_data/SRR1956527_2.fastq --reorder -S SRR1956527_2.sam
hisat2 -x hisat2/mm10_index --threads 8 ../original_data/SRR1956528_1.fastq --reorder -S SRR1956528_1.sam
hisat2 -x hisat2/mm10_index --threads 8 ../original_data/SRR1956528_2.fastq --reorder -S SRR1956528_2.sam
hisat2 -x hisat2/mm10_index --threads 8 ../original_data/SRR1956529_1.fastq --reorder -S SRR1956529_1.sam
hisat2 -x hisat2/mm10_index --threads 8 ../original_data/SRR1956529_2.fastq --reorder -S SRR1956529_2.sam
hisat2 -x hisat2/mm10_index --threads 8 -U ../original_data/SRR1956527_1.fastq.gz --reorder | samtools view -Shb - > SRR1956527_1.bam
hisat2 -x hisat2/mm10_index --threads 8 -U ../original_data/SRR1956527_2.fastq.gz --reorder | samtools view -Shb - > SRR1956527_2.bam
hisat2 -x hisat2/mm10_index --threads 8 -U ../original_data/SRR1956528_1.fastq.gz --reorder | samtools view -Shb - > SRR1956528_1.bam
hisat2 -x hisat2/mm10_index --threads 8 -U ../original_data/SRR1956528_2.fastq.gz --reorder | samtools view -Shb - > SRR1956528_2.bam
hisat2 -x hisat2/mm10_index --threads 8 -U ../original_data/SRR1956529_1.fastq.gz --reorder | samtools view -Shb - > SRR1956529_1.bam
hisat2 -x hisat2/mm10_index --threads 8 -U ../original_data/SRR1956529_2.fastq.gz --reorder | samtools view -Shb - > SRR1956529_2.bam
bowtie2
^^^^^^^^

.. code:: bash
bowtie2 -x bowtie2/mm10_index --threads 8 ../original_data/SRR1956527_1.fastq --reorder -S SRR1956527_1.sam
bowtie2 -x bowtie2/mm10_index --threads 8 ../original_data/SRR1956527_2.fastq --reorder -S SRR1956527_2.sam
bowtie2 -x bowtie2/mm10_index --threads 8 ../original_data/SRR1956528_1.fastq --reorder -S SRR1956528_1.sam
bowtie2 -x bowtie2/mm10_index --threads 8 ../original_data/SRR1956528_2.fastq --reorder -S SRR1956528_2.sam
bowtie2 -x bowtie2/mm10_index --threads 8 ../original_data/SRR1956529_1.fastq --reorder -S SRR1956529_1.sam
bowtie2 -x bowtie2/mm10_index --threads 8 ../original_data/SRR1956529_2.fastq --reorder -S SRR1956529_2.sam
bowtie2 -x bowtie2/mm10_index --threads 8 -U ../original_data/SRR1956527_1.fastq.gz --reorder | samtools view -Shb - > SRR1956527_1.bam
bowtie2 -x bowtie2/mm10_index --threads 8 -U ../original_data/SRR1956527_2.fastq.gz --reorder | samtools view -Shb - > SRR1956527_2.bam
bowtie2 -x bowtie2/mm10_index --threads 8 -U ../original_data/SRR1956528_1.fastq.gz --reorder | samtools view -Shb - > SRR1956528_1.bam
bowtie2 -x bowtie2/mm10_index --threads 8 -U ../original_data/SRR1956528_2.fastq.gz --reorder | samtools view -Shb - > SRR1956528_2.bam
bowtie2 -x bowtie2/mm10_index --threads 8 -U ../original_data/SRR1956529_1.fastq.gz --reorder | samtools view -Shb - > SRR1956529_1.bam
bowtie2 -x bowtie2/mm10_index --threads 8 -U ../original_data/SRR1956529_2.fastq.gz --reorder | samtools view -Shb - > SRR1956529_2.bam
.. code:: bash
bwa mem -A 1 -B 4 -E 50 -L 0 -t 8 bwa/mm10_index original_data/SRR1956527_1.fastq > SRR1956527_1.sam
bwa mem -A 1 -B 4 -E 50 -L 0 -t 8 bwa/mm10_index original_data/SRR1956527_2.fastq > SRR1956527_2.sam
bwa mem -A 1 -B 4 -E 50 -L 0 -t 8 bwa/mm10_index original_data/SRR1956528_1.fastq > SRR1956528_1.sam
bwa mem -A 1 -B 4 -E 50 -L 0 -t 8 bwa/mm10_index original_data/SRR1956528_2.fastq > SRR1956528_2.sam
bwa mem -A 1 -B 4 -E 50 -L 0 -t 8 bwa/mm10_index original_data/SRR1956529_1.fastq > SRR1956529_1.sam
bwa mem -A 1 -B 4 -E 50 -L 0 -t 8 bwa/mm10_index original_data/SRR1956529_2.fastq > SRR1956529_2.sam
bwa mem -A 1 -B 4 -E 50 -L 0 -t 8 bwa/mm10_index original_data/SRR1956527_1.fastq.gz | samtools view -Shb - > SRR1956527_1.bam
bwa mem -A 1 -B 4 -E 50 -L 0 -t 8 bwa/mm10_index original_data/SRR1956527_2.fastq.gz | samtools view -Shb - > SRR1956527_2.bam
bwa mem -A 1 -B 4 -E 50 -L 0 -t 8 bwa/mm10_index original_data/SRR1956528_1.fastq.gz | samtools view -Shb - > SRR1956528_1.bam
bwa mem -A 1 -B 4 -E 50 -L 0 -t 8 bwa/mm10_index original_data/SRR1956528_2.fastq.gz | samtools view -Shb - > SRR1956528_2.bam
bwa mem -A 1 -B 4 -E 50 -L 0 -t 8 bwa/mm10_index original_data/SRR1956529_1.fastq.gz | samtools view -Shb - > SRR1956529_1.bam
bwa mem -A 1 -B 4 -E 50 -L 0 -t 8 bwa/mm10_index original_data/SRR1956529_2.fastq.gz | samtools view -Shb - > SRR1956529_2.bam
Build, visualize and correct Hi-C matrix
Expand Down Expand Up @@ -165,9 +165,9 @@ To build the Hi-C matrices:
.. code:: bash
mkdir hicMatrix
hicBuildMatrix --samFiles SRR1956527_1.sam SRR1956527_2.sam --binSize 10000 --restrictionSequence GATC --outBam SRR1956527_ref.bam --outFileName hicMatrix/SRR1956527_10kb.h5 --QCfolder hicMatrix/SRR1956527_10kb_QC --threads 8 --inputBufferSize 400000
hicBuildMatrix --samFiles SRR1956528_1.sam SRR1956528_2.sam --binSize 10000 --restrictionSequence GATC --outBam SRR1956528_ref.bam --outFileName hicMatrix/SRR1956528_10kb.h5 --QCfolder hicMatrix/SRR1956528_10kb_QC --threads 8 --inputBufferSize 400000
hicBuildMatrix --samFiles SRR1956529_1.sam SRR1956529_2.sam --binSize 10000 --restrictionSequence GATC --outBam SRR1956529_ref.bam --outFileName hicMatrix/SRR1956529_10kb.h5 --QCfolder hicMatrix/SRR1956529_10kb_QC --threads 8 --inputBufferSize 400000
hicBuildMatrix --samFiles SRR1956527_1.bam SRR1956527_2.bam --binSize 10000 --restrictionSequence GATC --outBam SRR1956527_ref.bam --outFileName hicMatrix/SRR1956527_10kb.h5 --QCfolder hicMatrix/SRR1956527_10kb_QC --threads 8 --inputBufferSize 400000
hicBuildMatrix --samFiles SRR1956528_1.bam SRR1956528_2.bam --binSize 10000 --restrictionSequence GATC --outBam SRR1956528_ref.bam --outFileName hicMatrix/SRR1956528_10kb.h5 --QCfolder hicMatrix/SRR1956528_10kb_QC --threads 8 --inputBufferSize 400000
hicBuildMatrix --samFiles SRR1956529_1.bam SRR1956529_2.bam --binSize 10000 --restrictionSequence GATC --outBam SRR1956529_ref.bam --outFileName hicMatrix/SRR1956529_10kb.h5 --QCfolder hicMatrix/SRR1956529_10kb_QC --threads 8 --inputBufferSize 400000
The output bam files show that we have around 34M, 54M and 58M selected
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