User: NAVID.BAVI

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NAVID.BAVI0
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Posts by NAVID.BAVI

<prev • 10 results • page 1 of 1 • next >
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Comment: C: HISAT2 SRR error
... Thanks, yes that's why, though a bit surprised by such restrictions. ...
written 14 days ago by NAVID.BAVI0
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HISAT2 SRR error
... Hi all, I'm trying to run hisat2 for aligning an available DRG rna seq using the following command: /data/local/hisat2-2.1.0/hisat2 -p 4 -q --dta --known-splicesite-infile $ANNOT/splicesites.txt --dta-cufflinks -x $HST2IDX --sra-acc SRR1330498 -S $WORKDIR/SRR1330498.sam However I get the fol ...
srr sra alignment rna-seq hisat2 written 18 days ago by NAVID.BAVI0 • updated 18 days ago by genomax58k
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Comment: C: Transcriptome analysis using tophat and bowtie
... Thank you, I'll consider using other packages as well provided I can find step by step tutorials for them. Cheers, N ...
written 8 weeks ago by NAVID.BAVI0
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Comment: C: Transcriptome analysis using tophat and bowtie
... Thanks a lot for the guidelines, I'll go through all the comments, as suggested. ...
written 8 weeks ago by NAVID.BAVI0
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Transcriptome analysis using tophat and bowtie
... Hi everyone, I'm a new user and have been trying to reanalyze a zebrafish RNA seq data from another study which are available in fastq files (SRA tools were used). However, I've been stuck on the use of tophat for a while and I cannot move forward. I'm running tophat through: module load bowti ...
software error bowtieindex tophat bowtie written 8 weeks ago by NAVID.BAVI0 • updated 8 weeks ago by RamRS19k
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Comment: C: Getting BAM files using Bowtie
... Thanks a lot for the help. It seems to be working with adding the flag -f. My best N ...
written 3 months ago by NAVID.BAVI0
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Getting BAM files using Bowtie
... Hi everyone, I have a set of merged unpaired reads (RNA seq data) that are in ASCII text format (e.g. sample1_MERGED). I've used Megahit to co-assemble them and get the contig files. Now I wish to get the BAM files using Bowtie but I am not sure how it is done properly for unpaired reads like thos ...
software error assembly bowtie rna-seq mapping written 3 months ago by NAVID.BAVI0 • updated 3 months ago by h.mon21k
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Comment: C: co-assemble Merged reads using Megahit
... Thank you for replying. I do need to exclude the reads with mismatch before using Megahit. h.mon comment actually worked. Cheers Navid ...
written 3 months ago by NAVID.BAVI0
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Comment: C: co-assemble Merged reads using Megahit
... Thanks a lot, it worked! I actually missed this point from the manual. My very best, Navid ...
written 3 months ago by NAVID.BAVI0
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co-assemble Merged reads using Megahit
... Hi everyone, I have 13 RNA seq datasets (demultiplexed fastq files) and I am trying to co-assemble them into contigs that are at least 1000 kb long and eventually perform a differential transcriptome analysis. For start, I did a quality check with "illumina-utils" package and merged the reads wit ...
assembly sequence rna-seq megahit merged-reads written 3 months ago by NAVID.BAVI0

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