User: nanoide

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nanoide40
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Posts by nanoide

<prev • 56 results • page 1 of 6 • next >
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Comment: C: How to add a flag to a sam/bam file
... Thanks for your answer. I don't have the code for the creation of this file, but I believe the function splitBam in the ATACSeqQC Bioconductor package was used, to get mononucleosome bam files from the whole file. I think it's probably an issue of the tags provided to that function. I have tried sam ...
written 18 days ago by nanoide40
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How to add a flag to a sam/bam file
... Hi there. So I'm working with paired sam/bam files, filtering and subsetting them. I have noticed in some step of the filtering I have lost the flag "properly paired" when checking with samtools flagstat. And apparently a software (danpos) is requiring this field in samtools flagstat to be filled. ...
flag samtools atac-seq filtering written 18 days ago by nanoide40
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Comment: C: ATAC-seq TSS profile plot interpretation
... Thanks for the very useful advice. Regards ...
written 12 weeks ago by nanoide40
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Comment: C: ATAC-seq TSS profile plot interpretation
... Thank you for your response! For now just following the first steps of a pipeline and doing quality control. So this was just for descriptive purposes. Thanks for your time and sharing your expertise ...
written 12 weeks ago by nanoide40
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Comment: C: ATAC-seq V-plot interpretation
... It was used on a pipeline I inherited, and seems to be similar to the step checking enrichment at TSS in other pipelines, so I just kept using it. In any case, it seems then like a good idea to use a more updated one. Any suggestions? Thanks ...
written 12 weeks ago by nanoide40
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Comment: C: ATAC-seq V-plot interpretation
... Thanks you for your edit and your clarification. It seems I was indeed mistaken calling this V-plot, I guess I was misled by the title and header of the script. Apologies for that. I think in other places and pipelines this is referred as "TSS enrichment" plot, with distance in the x axis and insert ...
written 12 weeks ago by nanoide40
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ATAC-seq TSS profile plot interpretation
... Hi there, So I'm working with ATAC-seq data and I have applied the pymakeVplot (https://github.com/jinxu9/ATACseq/blob/master/libs/pyMakeVplot.py) code to generate a V-plot centered at TSSs. So this is what I get: ![enter image description here][1] My question is regarding the interpretation and ...
tss atac-seq v-plot written 12 weeks ago by nanoide40
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HaplotypeCallerSpark How to use
... Hi all. So I wanted to try the HaplotypeCaller Spark implementation in GATK4. I'm aware it's beta and not totally recomended yet, but we want to try it. So I wanted to ask about the usage, I looked for documentation but I'm not clear on some errors I'm getting. I also wanted to ask about the --stri ...
gatk snp written 5 months ago by nanoide40 • updated 4 months ago by lakhujanivijay4.7k
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Comment: C: Merging the output of salmon for RNA-seq counting with paired-end and single-end
... Thank you all for useful suggestions ...
written 6 months ago by nanoide40
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Merging the output of salmon for RNA-seq counting with paired-end and single-end reads simultaneously
... Hi all So, I'm working with some RNA-seq raw reads, both paired end (2 x 150 bp) and single-end (1x75 bp). These are coming from the same samples, but sequenced differently in 2 rounds. I want to get counts for each at the trasncript level using salmon. For DEseq2 differential expression analysis ...
paired-end salmon rna-seq single-end written 6 months ago by nanoide40

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Popular Question 18 days ago, created a question with more than 1,000 views. For TPKM vs FPKM
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