User: kuhelikadas1995

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Posts by kuhelikadas1995

<prev • 11 results • page 1 of 2 • next >
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library type selection problem
... my paired end rna seq data includes solexa library preparation, and illumina hiseq 2000... can't understand by any means that whether to use `fr-unstranded`or `fr-firststrand`or `fr-secondstrand`for transcript assembling by cufflinks tool. ...
rna-seq written 2 days ago by kuhelikadas19950 • updated 2 days ago by h.mon27k
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Comment: C: transcript assembling problem by cufflinks
... i am using cufflinks version 2.2.1 ...
written 3 days ago by kuhelikadas19950
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Comment: C: transcript assembling problem by cufflinks
... what difference would it make?? moreover during hisat2 alignmnt i used the command "--dta-cufflinks" which does the job specifically for cufflinks.. ...
written 4 days ago by kuhelikadas19950
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transcript assembling problem by cufflinks
... after alignmnt by hisat2 tool and generation of SAM ,BAM and sorted BAM files,i gave this command for transcripts assembling: cufflinks -o SRR1131119.sam -G Homo_sapiens.GRCh38.97.gff3 --library-type fr-firststrand --no-update-check --upper-quartile-norm SRR1131119_sorted.bam then this happen ...
tool rna-seq written 4 days ago by kuhelikadas19950 • updated 4 days ago by h.mon27k
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Comment: C: SAM file generation problem
... initially i had used the command > `cutadapt -a AGATCGGAAGA....and so on` I mean i skipped the "-A adapter2" part keeping rest of the command same , initially for trimming.. but that command is for single end data..whereas my data is of paired end..That time SAM files generated were of 4.4GB ea ...
written 13 days ago by kuhelikadas19950
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Comment: C: SAM file generation problem
... yeah.. and it did generate the indexes for genome by myself.. nothing was mentioned about the adapteer sequence.. it used AGATCGGAAGA.. for both forward and reverse end reads. should i use AGATCGGAAGAGC as the adapter sequence fr both the end reads?? ...
written 13 days ago by kuhelikadas19950
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Comment: C: SAM file generation problem
... raw data for r1 read is of size 502.3MB and that of r2 is of 498.8MB.. trimmed data for r1 is of 489.6MB and that of r2 is 486.6MB.. moreover, applying `-q 30`before or after made no difference. Size of reference genome is 1.1GB(zipped file) and 4.5GB(when unzipped) ...
written 14 days ago by kuhelikadas19950
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Comment: C: SAM file generation problem
... I accepted the answer nd tried.. then saw that i didnt work.. ...
written 14 days ago by kuhelikadas19950
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Comment: A: SAM file generation problem
... done. but it didnot work. same problem. no alignmnt done. ...
written 14 days ago by kuhelikadas19950
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Comment: C: SAM file generation problem
... nohup hisat2 --dta -cufflinks -x ../5.Reference_genome/genome -1 ../4.Trimmed_fastq/SRR1131659_Trimmed_1.fastq.gz -2 ../4.Trimmed_fastq/SRR1131659_Trimmed_2.fastq.gz -S SRR1131659.sam -p 20 & this was the command used for aligning the adapter trimmed fastq files against human refernce genom ...
written 14 days ago by kuhelikadas19950 • updated 14 days ago by genomax70k

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