User: shounak.chakraborty1990

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Posts by shounak.chakraborty1990

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Extract all sub-fragments from a gtf
... Hi Everyone, I am trying to find out all transcripts that are a subfragment of any other transcript from a gtf file. By subfragment, I mean completely contained in another transcript. I used gffCompare but it does not work, since I compare a particular gtf to itself and gffcompare reports all tran ...
assembly rna-seq written 9 days ago by shounak.chakraborty19900
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Comment: C: Merge FastQ Files
... Thanks. This works really good and fast. ...
written 15 months ago by shounak.chakraborty19900
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Comment: C: Merge FastQ Files
... The previous thread talks mostly about using cat and glob patterns. There is also a mention for a particular tool but it does not seem to merge in his specific way. Regarding alignment, yeah I can merge it later but I need to merge the fastQ files before alignment :) ...
written 15 months ago by shounak.chakraborty19900
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Comment: C: Merge FastQ Files
... Those are the last four lines of the example after which I put a couple of dots to indicate that the process continues. It is important to note that one read consists of four lines in a file. The first lines of the example explain the merging process quite clearly. ...
written 15 months ago by shounak.chakraborty19900
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Comment: C: Merge FastQ Files
... It is important since I am going to run Kallisto on the merged file and Kallisto estimates the fragment length distribution but it uses only a certain number of reads from the top to do that. So if I use cat then the reads in the other files are not being used to estimate the fragment length. So I n ...
written 15 months ago by shounak.chakraborty19900
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Comment: C: Merge FastQ Files
... Using cat on the files results a file with all the reads from file1 followed by the reads from file2 and so on and so forth. However I want the first seven reads from in my merged file to be the first reads from all the seven files, the second seven reads to be the second reads from the seven files ...
written 15 months ago by shounak.chakraborty19900
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Merge FastQ Files
... I have 7 FastQ files and I want to merge them into one in the following way: >File1 line1 >File1 line2 >File1 line3 >File1 line4 >File2 line1 >File2 line2 >File2 line3 >File2 line4 >File3 line1 ...
fastq rna-seq written 15 months ago by shounak.chakraborty19900 • updated 4 months ago by Biostar ♦♦ 20

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