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>>> Writing bisulfite mapping results to pTregrep1_P_R1.fq.gz_bismark_bt2_pe.bam
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Hi,
I am new in bisulfite sequencing analysis and is learning Bismark.But I got a problem in installing the software.
I have Bowtie2 and samtools in my path, but after I un-tar the package by "…
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Hi,
I am trying to map paired end fastq files from bisulfite HIV LTR. Therefore, the mapping step implies using the HIV LTR region as a reference and not the human genome
I tried to create a ref.dbi…
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Hi,
I'm having issues. When I run bismark methylation extraction it keeps failing on me.
The issue seems to be around this
```
The strand information was neither + nor -:
```
Much of the …
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Can I run picard as a standalone program as follows?
picard CollectInsertSizeMetrics I=Sons_Aligned_Bam_File.bam O=insertmetrics.out H=insertSizeHistogram.pdf
Do i have to write a yaml file for th…
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Published: https://doi.org/10.1186/s13059-017-1189-z
Preprint: https://dx.doi.org/10.1101/055715
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Hi,
Recently I've tried using bsmap to align bisulfite sequencing data, I found something I can't understand when looking at the output bam file:
```
ST-E00206:158:HVLMYCCXX:7:121 161 # chrM 156…
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Hi,
While doing step 2 ‘Call consensus reads (fgbio’s CallMolecularConsensusReads), map them (with bwa-mem), then filter them (fgbio’s FilterConsensusReads).’, I run into trouble.
My command lin…
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Hello Felix,
I have a little problem doing the methylation extraction in my paired end data.
When I do the bismark_methylation_extractor, all works fine except one thing. This is the output:
…
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Hi,
I am running `bwameth.py tabulate` on an Ecoli bisulfite treated sample aligned with bismark/bowtie2.
I was getting no methylation calls with the default parameters, so I changed to `--context a…