Moderator: ATpoint

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ATpoint26k
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Posts by ATpoint

<prev • 3,633 results • page 2 of 364 • next >
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Comment: C: Correlation of two ChIP-seq signals?
... Can you add some representative code and screenshots? With just words it is difficult to reproduce / understand what you see or think to see. By-eye interpretation is probematic. How many regions did you check by eye and and how many regions were included in the calculation, aka is your by-eye analy ...
written 2 days ago by ATpoint26k
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Comment: C: fastqc per base sequence content and kmer content fail
... https://www.biostars.org/p/180962/ https://www.biostars.org/p/91701/ ...
written 3 days ago by ATpoint26k
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Comment: C: Enhancer regions for rn5
... Hello bioinfc37! We believe that this post does not fit the main topic of this site. Unspecific. OP never followed up. For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with. If you disagree please tell us why in a r ...
written 3 days ago by ATpoint26k
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Comment: C: RNA seq query
... There is no computational method that will magically render an underpowered experiment to be well-powered. Your experimental design is flawed as 1 vs 1 is not statistically solid. Nothing you can do about it, sorry. Best you can do is some exploratory analysis. Please read previous posts on how to d ...
written 3 days ago by ATpoint26k
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Comment: C: Empty output when use HOMER annotatePeak.pl
... Best guess, the folder with these scripts is not in `$PATH`. ...
written 3 days ago by ATpoint26k
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Answer: A: Trimming Adapters for RNA-SEQ (Quality Check)
... Actually it is pretty trivial. Run `fastqc` which will tell you if there are adapter contaminations or not. If not, your are fine. If so, you simply trim the sequence it identified. In 99% of cases for standard RNA-seq it is the normal TruSeq adapter which you could look up by googling it (there are ...
written 4 days ago by ATpoint26k
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Answer: A: ERROR in sam to bam conversion
... It is not recommended to directly dump files, be it fastq or sam from NCBI. The connection is too unstable (in my experience) and this is exactly what you see. This file is most likely also raw (unaligned) data so there is little point in transformating it to BAM. Better get raw data and align yours ...
written 4 days ago by ATpoint26k
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Comment: C: Differential expression tool that can take TPM as input?
... None of it is ideal. You should start from raw counts if possible. If not and TPM is the only thing you have then what does it matter, results will anyway be unreliable, so interpret them with care and try to validate the important genes with either experiments or published RNA-seq data in a similar ...
written 4 days ago by ATpoint26k
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Answer: A: Differential expression tool that can take TPM as input?
... https://support.bioconductor.org/p/126817/ Please also use the search function and google as this has been addressed literally dozens of times. ...
written 4 days ago by ATpoint26k
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Answer: A: Using xargs to tabix each line of a bed to a vcf
... The syntax of tabix is wrong. It needs to be `tabix (options) file.vcf.gz {regions}`: awk '{print $1":"($2+1)"-"$3}' CHR21_RegionsforBeagle.bed | xargs -n1 tabix -fh 21.ACANAFCR_sorted.vcf.gz {} but I am not sure if the redirection to the file will work. What will work is the same with `parall ...
written 4 days ago by ATpoint26k

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Teacher 1 day ago, created an answer with at least 3 up-votes. For C: Detect repeats problematic for PCR
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Scholar 4 days ago, created an answer that has been accepted. For C: Analyzing Whole exome Seq for mouse
Popular Question 4 days ago, created a question with more than 1,000 views. For SVtyper on lumpyexpress VCF: somatic-germline
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Scholar 12 days ago, created an answer that has been accepted. For C: Analyzing Whole exome Seq for mouse
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