User: goodez

gravatar for goodez
goodez420
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M.S. in Bioinformatics & Genomics. Always looking to expand my programming experience.

Posts by goodez

<prev • 122 results • page 1 of 13 • next >
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Comment: C: Issues with Marking Duplicates in Picard
... Sorry to hear that. I personally have had issues every time I've tried to use any Picard tool... Do you require duplicate removal in your analysis? Removing duplicates is often unnecessary and can even falsely remove unique reads. ...
written 7 days ago by goodez420
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Comment: C: Issues with Marking Duplicates in Picard
... Weird. Maybe because that output file already exists, and doesn't want to overwrite it? Try this as well. You shouldn't have to specify bam format, but I don't know what version of software you're using. `samtools sort -O bam -o S1_sorted.bam S1_merged.bam` Run exactly that. It shouldn't give err ...
written 7 days ago by goodez420
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Answer: A: Issues with Marking Duplicates in Picard
... First, I don't totally understand what the "singles" file is. I would just stick with the forward and reverse fastq files (R1 and R2). Now for combining samples from multiple lanes... I usually merge the fastq files before aligning. I first check their quality using FastQC. It is also okay to comb ...
written 7 days ago by goodez420
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Answer: A: Bowtie2 reports no secondary alignments
... Oops... I know what is happening now. Bowtie2, by default, only reports the best alignment. This is why I have zero secondary alignments in my bam file, despite having many "multi-mappers". This information was in the **Reporting** section of the [bowtie2 manual][1]. I think the manual could be mor ...
written 7 days ago by goodez420
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Bowtie2 reports no secondary alignments
... This has been bugging me for awhile now. I know there are multiple mapping reads in my alignments, but bowtie2 does not assign the 256 flag for any of my reads. Bowtie2 says in the manual that is should be doing this: > Each reported read or pair alignment beyond the first has the SAM > ‘seco ...
bowtie2 alignment written 8 days ago by goodez420
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Answer: A: Pindel -x option
... -n/--min_NT_size only report inserted (NT) sequences in deletions greater than this size (default 50) -v/--min_inversion_size only report inversions greater than this number of bases (default 50) ...
written 27 days ago by goodez420
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Comment: C: Where to find a list of stress response genes?
... Overall they correlate very well. It's not a huge concern for us if this is just limited to a small subset of genes. We aren't doing differential expression. We're looking at the general profile of Pol II transcription with and without a treatment. If I remove these genes, and still see the differen ...
written 28 days ago by goodez420
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Comment: C: Where to find a list of stress response genes?
... I don't have counts. This is ChIP-seq data of Pol II. For the most part the replicates agree with each other, but they think the heat shock genes are activated in one replicate, which affects our average gene metaplot, for example. I was just hoping there was some source of heat shock genes existing ...
written 28 days ago by goodez420
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Comment: C: Where to find a list of stress response genes?
... Thanks for the idea. I do agree it is general. However I really do not have more details. I was simply asked to "remove stress response genes" because the biology expert thinks one of our replicates was subjected to some kind of stress during the experiment. Let's assume I just want to focus on he ...
written 28 days ago by goodez420
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Where to find a list of stress response genes?
... I need a list of heat shock genes to exclude from my analysis. I'm working with hg38 genome. I'm not sure the best approach to find all heat shock genes, or if I can download it from somewhere. Thanks. EDIT -- Not just heat shock, perhaps more generally I need "stress response genes". ...
gene annotation written 28 days ago by goodez420

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Scholar 7 days ago, created an answer that has been accepted. For A: Meaning of Decimal points in ENST notation
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