User: compugene

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compugene0
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Posts by compugene

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Comment: C: awk help to print lines when the columns are non zeros
... Ok sure, thanks Kshama. ...
written 10 days ago by compugene0
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Comment: C: awk help to print lines when th columns are non zeros
... Also to add to my previous email. There is tons of text processing that happens in NGS and it is important to somehow link computational questions to bioinformatics/ngs portal. If this does not fit the realm currently, I strongly feel one should come up with one such,unless there is a portal already ...
written 10 days ago by compugene0
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Comment: C: awk help to print lines when th columns are non zeros
... I disagree. When we get transcripts count file from htseq or refseq etc,it spits out genenames with columns of a value. We would then go ahead and delete lines which has zeros across all columns. I did not want to post my data set and values on the post and hence gave random names. It is bioinfor ...
written 10 days ago by compugene0 • updated 10 days ago by Ram12k
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(Closed) awk help to print lines when the columns are non zeros
... Hi I have a file with the following format: filename is foo.txt abcd 1 0 0 2 abef 2 0 0 0 able 2 1 2 0 able 1 0 0 0 efgh 0 0 0 0 I wrote an awk script to delete the row with all columns with 0. But I am getting syntax error. SO I am sure this is very simple. Please can anytim ...
next-gen written 10 days ago by compugene0 • updated 10 days ago by Ram12k
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Answer: A: Pirnas Sequence Files In Fasta Format For Rat And Mapping Small Rna Seq Reads
... I have done some similar work with my small RNA sequences. I used proTRAC software to identify any piRNA clusters. proTRAC is developed by Dr.David Rosenkranz's group. THis can be run on command line or as a user interface. I have used command line options The pdf for the user documentation mentions ...
written 2.5 years ago by compugene0
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Comment: C: SAM File target extraction
... Hi tangming2005 Thanks for the reply . I was looking into tabix earlier, the reason I posted this question is because, I am not really interested in the coordinates of the reference region where my sequence maps to, but I would like to retrieve the corresponding sequence itself ( string of ATGCs) t ...
written 3.2 years ago by compugene0
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SAM File target extraction
... Hi all, Is there a way to extract the corresponding target sequence from an bam or SAM alignment produced by novoalign software? or bowtie? Thanks Geneart. ...
alignment written 3.2 years ago by compugene0 • updated 3.2 years ago by tangming20052.1k
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Comment: A: How Do I Convert From Sam To Eland Format?
... Hi KCC , was wondering if you had an opportunity to test the pyicos suggested by Vikas Bansal? I am currently trying to convert SAM to eland to use in proTRAC software. That software specifes a eland format file generated by seqmap output using pyicos. I tried using Pyicos , but the eland format I g ...
written 3.2 years ago by compugene0
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SAM to eland conversion
... Hello Biostars, I was trying out a new ( relatively ) software proTrac to map piRNA clusters. THe software calls for ELAND formatted files. In my quest for conversion tools I found pyicos to convert SAM to eland but the eland output had many fields than specified in the document for proTrac.Looks l ...
rna-seq written 3.2 years ago by compugene0 • updated 2.3 years ago by A. Domingues1.4k
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Comment: A: EdgeR toptags question
... Adding onto the reply I just uploaded ...... if everything looks fine based on what I uploaded it could have been that in my sample sets i could have just those genes being differentially expressed across both tagwise and common?? not sure if I phrased it correctly here , but just wanted to confirm ...
written 3.3 years ago by compugene0

Latest awards to compugene

Popular Question 2.5 years ago, created a question with more than 1,000 views. For SAM File target extraction
Popular Question 2.5 years ago, created a question with more than 1,000 views. For EdgeR toptags question
Popular Question 2.5 years ago, created a question with more than 1,000 views. For miRNA names from ensemble IDs

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