User: star

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star60
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Posts by star

<prev • 51 results • page 1 of 6 • next >
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Comment: C: How extract aligned exactly 1 time in Single end read?
... Good! Thanks !. it is working ...
written 2 days ago by star60
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How to extract aligned exactly 1 time in Single end read?
... I like to have exactly 1 match reads (6729690) from output of bowtie2 aligner. the blow cod is what I have used for aligning. bowtie2 --very-sensitive --score-min C,0,0 -p 8 -x Genome_Index input.fastq.gz -S output.sam 8506903 reads; of these: 8506903 (100.00%) were unpaired; of t ...
bowtie2 alignment bwa written 2 days ago by star60 • updated 2 days ago by zx87544.5k
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Comment: C: no exact read?
... @h.mon, thanks ! So , use grep _v xs:i, would be enought to extract 1 match reads? ...
written 3 days ago by star60
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Comment: C: no exact read?
... Dear Fin, No in this case is single end, you are right! So I should not use 0x2 and just removing xi:s would be fin, right? ...
written 3 days ago by star60
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no exact read?
... I have some ChIP-seq data with 36 bp read length and I have done aligning with bowtie2 with below cod: bowtie2 --very-sensitive --score-min C,0,0 -p 8 -x Genome_Index input.fastq.gz -S output.sam and then I have tried to extract only 1 exact match with below cod: samtools view -hf 0x2 o ...
R alignment chip-seq bwa bowtie2 written 3 days ago by star60
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Peak calling using macs2?
... I have paired end ChIP-seq data with 101 bp and 2 biological replicates for each one. I have done peak calling with macs2 but I have some questions about it. I also faced with an warning: WARNING @ Thu, 07 Jun 2018 17:06:05: #2 Since the d (197) calculated from paired-peaks are smaller than 2* ...
macs2 chip-seq peaks peak-calling written 10 days ago by star60 • updated 10 days ago by Ram15k
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Comment: C: how to consider batch effect in design matrix?
... @mon, Thanks for your reply. yes i removed the sample column but still have error. Thanks a lot for your links. ...
written 7 weeks ago by star60
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how to consider batch effect in design matrix?
... I have two set data, 4 samples with 2 replicates for each one from batch 1 and another 4 samples with 2 replicates from batch 2. I would like to remove batch effects from these samples and compare different methods together. I have done below commands but face with error: design ...
R design matrix edger differential expression written 7 weeks ago by star60
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find significant analysis?
... I have done Differential expression (DE) analysis and found 2212 DE genes in my data, then I found the overlap between my DE genes and some diseases related genes (e.g. ALS). ALS disease contains 1007 genes that 500 of those had overlap with DE genes. Now I would like to find these number are signif ...
R fisher.test statistic written 8 weeks ago by star60 • updated 8 weeks ago by Rasoul Godini0
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Design matrix for edge R analysis?
... I would like to compare Q method against L method, and I have considered 2 different contrasts (at the end), but I am not sure which on is correct? There are 2 different methods (Q and L) and from each one there are 2 biological replicates (L4,L6-L8 and Q3,Q5-Q7), and 2 technical replications from ...
R bioconductor limma edger statistics written 9 weeks ago by star60

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