User: yaminivadapally

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Posts by yaminivadapally

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about cuffdiff input and parameters
... i have 120 sample in which 60 are controls and 60 are diseased, i ran tophat, cufflinks and cuffmerge i have merged_asm.gtf file which is output of cuffmerge. i want to run cuffdiff to find differential expression how to give command for cuffdiff,which parameters should i use????? ...
rna-seq written 6 weeks ago by yaminivadapally0 • updated 6 weeks ago by kristoffer.vittingseerup1.0k
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Cuffmerge Error Duplicate Transcripts
... i want to merge cufflinks transcript.gtf files into a single file using cuffmerge the reference genome was downloaded from gencode am getting this error ... GFF Error: duplicate/invalid 'transcript' feature ID=ENST00000361547.6 [FAILED] Error: could not execute cuffcompare ...
rna-seq written 8 weeks ago by yaminivadapally0 • updated 8 weeks ago by finswimmer8.2k
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Comment: A: perl script for mapping two files
... NO. there are 240 files of both outputs i need to map correponding 2 files as single output ...
written 9 weeks ago by yaminivadapally0
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Comment: A: perl script for mapping two files
... cpcout- I want headers whose score <-1 example file : hg38_ct_UserTrack_3545_CUFF.4097.1 27422 noncoding -1.00386 hg38_ct_UserTrack_3545_CUFF.4100.1 1203 noncoding -0.783661 hg38_ct_UserTrack_3545_CUFF.5257.2 75281 noncoding -0.560148 hg38_ct_UserTrack_3545_CUFF.5257.1 93082 non ...
written 9 weeks ago by yaminivadapally0 • updated 9 weeks ago by zx87546.1k
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perl script for mapping two files
... How can I map the two files one is output of getorf and another is cpc output, i want a single file as output which has score < -1 from cpc output and seq which has greater than 30 amino acids from getorf output as a single output file ...
perl rna-seq written 9 weeks ago by yaminivadapally0 • updated 9 weeks ago by zx87546.1k
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(Closed) CPC(coding potential calculator) ERROR
... > Can't open file (/blastx.feat1): No such file or directory at > ./add_missing_entries.pl line 10. cat: /ff.fa1: No such file or > directory WHY AM I GETTING THIS ERROR? ...
rna-seq written 10 weeks ago by yaminivadapally0 • updated 9 weeks ago by zx87546.1k
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about bioperl script for extracting sequences from a fasta file(get orf output file) with ids which has less than 30 amino acids
... i want the script to get sequences from a fasta file which is an output of jemboss(get orf) which has less than 30 amino acids ...
python bioperl rna-seq written 10 weeks ago by yaminivadapally0 • updated 10 weeks ago by Nitin Narwade330
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Perl script for discarding sequences less than 200 nucleotides before running CPC in rnaseq analysis
... Ii want the perl script to discard sequences less than 200 nts from fasta file to run CPC ...
perl rna-seq written 11 weeks ago by yaminivadapally0 • updated 9 weeks ago by zx87546.1k
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About aligment in RNASeq analysis
... How many output files are generated in tophat2 alignment if i have given 5 input reads with reference genome for alignment, will i get 5 output files for every read or only a single file? ...
alignment rna-seq written 3 months ago by yaminivadapally0 • updated 3 months ago by k.kathirvel93170

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