User: Illinu

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Illinu90
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Posts by Illinu

<prev • 38 results • page 1 of 4 • next >
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Answer: A: All CpG sites in human genome RRBS
... Hi Pin.Bioinf, If you are still interested, you can email services@diagenode.com and they can give you a list of all CpGs detected in human samples with the Diagenode Premium RRBS Kit. Best, Sol ...
written 8 months ago by Illinu90
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Comment: C: Overrepresented % different between PE reads
... Hi h.mon, thanks for replying. I thought about that too but both reads have great quality scores accross the whole read. Both reads go down slighy towards the last 10 bp but the lowest phred score is around 34 and there are some error bars a bit lower in read 2 than in read 1. But I have a hard time ...
written 9 months ago by Illinu90
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Overrepresented % different between PE reads
... Hi, I have an RNA-Seq dataset from a library with average fragment size 250 bp that was sequenced in PE150 mode. The fastqc report shows a high amount of overrepresented sequences marked with no hit. What is puzzling is that the percentage of overrepresented sequences is very different between rea ...
fastqc rna-seq overrepresented written 9 months ago by Illinu90
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Comment: C: 12th International Conference on Advancements in Bioinformatics and Drug Discove
... Yes, please what do you mean by that? ...
written 14 months ago by Illinu90
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Answer: A: obtaining unique peaks in DiffBind
... Hi there, and thank you all for your very helpful answers. I thought of an approach for this problem and wanted to get your input. I think the trick is using the min.overlap option. If I understood well, setting a minimum overlap of 70% (min.overlap = 0.7) means that the peaks would be considered ...
written 14 months ago by Illinu90
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obtaining unique peaks in DiffBind
... Hi, I am using DiffBind for ChIP-Seq differential binding analysis. I want to use the occupancy analysis to extract peaks that are unique to one group and are absent in the other. I run the following command and I understand that the analysis outputs peaks that are present in at least 70% of the s ...
diffbind chip-seq differential written 16 months ago by Illinu90
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Comment: C: too many adj pvalues = 1
... Hi Devon, It just seems weird that the test finds insignificant Gene A between T and C for genotype B, when it goes from 2000 to 8000 counts with small error bars. To me there is a clear induction of this gene by the treatment compared to genotype 1. But the test considers this difference as not si ...
written 2.5 years ago by Illinu90
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too many adj pvalues = 1
... Hi, While analyzing a set of DEGs resulting from DESeq2, I noticed for some genes that were I 'see' differences they are not significant, but then another gene with similar behaviour, the difference is significant. They both come from different comparisons, the former with 6 replicates and the late ...
p-value deseq2 rna-seq written 2.5 years ago by Illinu90 • updated 2.5 years ago by Devon Ryan92k
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Answer: A: emtpy bcf file
... This was corrected at the mpileup step with -A option samtools mpileup -ug -A -f thal.fasta $bname-thal.nodup.sorted.bam > $bname-thal.bcf -A, --count-orphans Do not skip anomalous read pairs in variant calling. Maybe this is because the sequences I used as reference are short and the p ...
written 2.7 years ago by Illinu90
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Comment: C: emtpy bcf file
... Thanks @Pierre, I normally run the pipeline for some commands, some of those intermediate files I need for other tasks. But in the script above I am testing this way to see at what step it fails. So far up to the *.nodup.sorted.bam it works well, that's how I know that it is the bcf file that is not ...
written 2.8 years ago by Illinu90

Latest awards to Illinu

Popular Question 14 months ago, created a question with more than 1,000 views. For grep unexpected behaviour
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Great Question 2.5 years ago, created a question with more than 5,000 views. For Python: count how many lines have a specific word
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Python: count how many lines have a specific word
Epic Question 3.4 years ago, created a question with more than 10,000 views. For filter out multiple rows based on values in columns - perl and R attempt
Great Question 4.4 years ago, created a question with more than 5,000 views. For filter out multiple rows based on values in columns - perl and R attempt
Popular Question 4.4 years ago, created a question with more than 1,000 views. For Python: count how many lines have a specific word
Popular Question 4.4 years ago, created a question with more than 1,000 views. For filter out multiple rows based on values in columns - perl and R attempt

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