Moderator: ATpoint

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ATpoint26k
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Posts by ATpoint

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Comment: C: StringTie error input file not sorted, even though it is
... Did you try sorting (no matter if you think it is or is not) sorted using `samtools` a representative BAM file and then try `stringtie` again? Did that work? Also please show the command that was used for sorting in the first place. ...
written 10 hours ago by ATpoint26k
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Comment: C: How do I know if I have DNA contamination in RNA-seq data?
... How high is it? As often there is no fixed cutoff. ...
written 11 hours ago by ATpoint26k
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Comment: C: RPKM with bowtie output
... Please read the manual and then come back with more specific questions while opening a new question, providing the necessary details. ...
written 14 hours ago by ATpoint26k
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Comment: C: Whole genome sequencing or whole exome sequencing- which is better and why?
... I strongly recommend that https://www.biostars.org/u/1987/ spends time on the basics of sequencing platforms and applications before making any business decisions on what kit/platform/strategy to use for the project. ...
written 15 hours ago by ATpoint26k
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Answer: A: bbmap reference mapping error
... > The index format has changed in this version of BBTools. Please delete the /ref/ directory and re-index from the reference fasta. Please read the error messages. It is clear what you have to do => re-index the genome if you want to stick with that version of the tool or use an older versio ...
written 17 hours ago by ATpoint26k
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Comment: C: Whole genome sequencing or whole exome sequencing- which is better and why?
... Adding on this, you should (and probably must) also choose between short and long read sequencing. As https://www.biostars.org/u/24526/ says some structural variants will be difficult or impossible to find with short reads whereas SNPs are the realm of short reads. ...
written 17 hours ago by ATpoint26k
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Comment: C: RNAseq differential expression analysis : relevance of Immunoglobulin genes enri
... Are these tumors which undergo (so the cells of origin) SHM? So essentially are these B-cell tumors? Can you also give some basic information about the treatment? Is it something that could activate an immune response? How early after the treatment have the specimen been collected? ...
written 1 day ago by ATpoint26k
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Comment: C: RNA seq and Invitro data not matching
... What is `Invitro`? qPCR? Please add details: How many replicates, what is the setup, does PCA indicate good reproducability between replicates? What is the tool you used for analysis? Also please show an MA-plot and highlight the gene you are interested in. Your experiment could simply be underpower ...
written 1 day ago by ATpoint26k
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Answer: A: Looking for advise on histone modification chip-seq analysis - 2 conditions
... What you want is a standard differential analysis. Look at tools such as `csaw` or `Diffbind` which are essentially wrappers for `DESeq2` and `edgeR`. The manuals cover all basic analysis steps. You input a count matrix and eventually get a list of regions with significant changes for H3K27me3 betwe ...
written 3 days ago by ATpoint26k
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Answer: C: RNA-seq Differential expression analysis show no differentially expressed genes
... Well, not sure how to further help you from the bioinformatics side. You simply have no DEGs based on the current setup plus that potential batch effect. Probably have to go back to the lab and repeat the experiment. Was the gene that you checked by qPCR well-expressed or is it on the very left of t ...
written 3 days ago by ATpoint26k

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Good Answer 1 day ago, created an answer that was upvoted at least 5 times. For C: Detect repeats problematic for PCR
Appreciated 1 day ago, created a post with more than 5 votes. For C: Detect repeats problematic for PCR
Teacher 1 day ago, created an answer with at least 3 up-votes. For C: Detect repeats problematic for PCR
Scholar 3 days ago, created an answer that has been accepted. For A: Fasta extraction from bed file
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Teacher 17 days ago, created an answer with at least 3 up-votes. For C: Detect repeats problematic for PCR
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Teacher 19 days ago, created an answer with at least 3 up-votes. For C: Detect repeats problematic for PCR
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Commentator 29 days ago, created a comment with at least 3 up-votes. For C: How to run the Deseq2 tool without replicates.
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