Rohit Satyam

Error executing process > 'MACS2_QC'

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Hi. I have a Single End MiSeq Chipseq runs(single replicate). My `design.csv` is as follows ``` group,replicate,fastq_1,fastq_2,antibody,control A1_IP,1,A1_S1_L001_R1_001.fastq.gz,,, C1_TF_Ab,1,C1_S2_L001_R1_001.fastq.gz,,TF,A1_IP E1_IgG_control,1,E1_S3_L001_R1_001.fastq.gz,,IgG,A1_IP G1_H3K27Ac_Ab,1,G1_S4_L001_R1_001.fastq.gz,,H3K27Ac,A1_IP ``` I tried running peak-calling using your nf-core pipeline...

Hi This is a feature request. Can you make `./gaas_fasta_statistics.pl` output a `csv` file or `tsv` file instead of a markdown format output. It's good for visual inspection of assembly...

Enrichmentbrowser rmd

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This Repo now contains RMD files in Vignette folder.

Using Strobealign for aligning RNAseq to recodonized gene

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Hi I have RNA-Seq data for a gene knockout produced by recodonization (see [here](https://academic.oup.com/bfg/article/18/5/281/5540241?login=true) for meaning because this is new to me). This gene has 4 exons but since the...

Fastp failing to detect adapters automatically

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For sme unknown reason, Fastp is failing to detect Universal adapters in sequence. Given wide popularity of this tool in nextflow workflows these days, this is urgent to address. I...

How to decide if the reversionSubstitutions are valid variants or not and whether to keep them?

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Hi I have a small query. When I primarily process my sample using `wf-artic` pipeline and the upload consensus fasta on nextclade, I do not obtain any private mutations. However,...

**Describe the bug** ``` AttributeError Traceback (most recent call last) Cell In[37], line 4 1 import magic 3 # Apply MAGIC for PCA data denoising ----> 4 magic_op = magic.MAGIC(random_state=random_seed,...

Hi I was trying to use bwa instead of bowtie2 But I get the following error ``` ========= F L O W C R A F T ========= Build mode...

bcftools ignores indel even when using --min-ireads 10

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I tried variant calling using bcftools using recommended settings for SARS-Cov-2 i.e. using `--ignore-overlaps --min-ireads 10` on my `ISeq Illumina` data. However, I can see that a deletion supported by...

Database to use for human RNASeq

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Which database should we use to remove rRNA from Human RNASeq dataset. I see that using default database `smr_v4.3_default_db.fasta` gives me similar results to what I get using ribodetector. However,...