User: Ram

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Ram130
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130
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Location:
Germany
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5 hours ago
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5 years, 5 months ago
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Bioinformatician

Posts by Ram

<prev • 68 results • page 1 of 7 • next >
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Comment: C: Confused about how to generate a consensus sequence after bwa
... I think first you can create consensus sequence and then align your reads using bwa. ...
written 3 days ago by Ram130
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Comment: C: STAR two -pass mode - lower alignment rate than one pass mode?
... As in STAR manual, it states: It does not increase the number of detected novel junctions, but allows to detect more splices reads mapping to novel junctions. The basic idea is to run 1st pass of STAR mapping with the usual parameters, then collect the junctions detected in the first pass, and use ...
written 3 days ago by Ram130
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Comment: C: Tool for categorization of each gene in list according to sub-cellular location
... I think for your query PANTHER-Gene list analysis would be the best solution. ...
written 3 days ago by Ram130
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Comment: C: Extract Hard-clipped and soft-clipped values from fifth column
... Yes ! Any idea how i can be able to achieve this ? ...
written 3 days ago by Ram130
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Comment: C: Extract Hard-clipped and soft-clipped values from fifth column
... I want a result like this : chr1 21730857 21730962 M00758:777:BKR4B:1:2103:25646:13282 45M105H chr1 179196716 179196743 M00758:777:BKR4B:1:2101:24687:24458 87H36M27H Thanks ! ...
written 3 days ago by Ram130 • updated 3 days ago by genomax59k
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Comment: C: Extract Hard-clipped and soft-clipped values from fifth column
... Here is the code : awk -F'\t' 'NR==FNR{arr[$1]++;next}{for(i=1; i<=NF; i++) if ($i in arr){a[i]++;}} { for (i in a) printf "%s\t", $i; printf "\n"}' file.bed ...
written 3 days ago by Ram130 • updated 3 days ago by genomax59k
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Extract Hard-clipped and soft-clipped values from fifth column
... Hello all, Is it possible to know how I can extract 105 hard-clipped base from fifth column and then add value 105 to end coordinate of chr1 ? As I tried with awk, but no success ! chr1 21730812 21730857 M00758:777:BKR4B:1:2103:25646:13282 45M105H chr1 179196680 179196716 M00758:777: ...
perl sequencing awk bash written 3 days ago by Ram130 • updated 3 days ago by Pierre Lindenbaum115k
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Comment: C: Extract chimeric reads
... Thanks for replying. Yes I am using bwa itself and I have the reads with SA tag. Does SA reads are considered to be chimeric reads ? Thanks a lot for your help. ...
written 27 days ago by Ram130
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Comment: C: Extract chimeric reads
... Hi Pierre, As I have solved the problem with environment. Is it possible to know if samjdk will work for single end reads ? ...
written 27 days ago by Ram130
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Comment: C: Extract chimeric reads
... Unable to locate an executable at "/Library/Java/JavaVirtualMachines/jdk1.8.0_181.jdk/Contents/Home/bin/java/bin/javac" (-1) ...
written 28 days ago by Ram130

Latest awards to Ram

Popular Question 12 weeks ago, created a question with more than 1,000 views. For Error in identification of genomic variants from RNA-seq.
Popular Question 8 months ago, created a question with more than 1,000 views. For Error when running Miso
Popular Question 8 months ago, created a question with more than 1,000 views. For Differential binding analysis
Popular Question 11 months ago, created a question with more than 1,000 views. For Error when running Miso
Good Question 2.3 years ago, asked a question that was upvoted at least 5 times. For How To Write Data In A Granges Object To A Bed File.
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Error when running Miso
Epic Question 2.5 years ago, created a question with more than 10,000 views. For How To Write Data In A Granges Object To A Bed File.
Appreciated 2.5 years ago, created a post with more than 5 votes. For How To Write Data In A Granges Object To A Bed File.
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Format Conversion: Pgf (Probe Group File) Format To Fastq
Great Question 3.5 years ago, created a question with more than 5,000 views. For How To Write Data In A Granges Object To A Bed File.
Student 3.5 years ago, asked a question with at least 3 up-votes. For How To Write Data In A Granges Object To A Bed File.
Popular Question 4.5 years ago, created a question with more than 1,000 views. For How To Write Data In A Granges Object To A Bed File.

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