User: waqaskhokhar999

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Posts by waqaskhokhar999

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Comment: C: Alignment of single-ended library distributed among different lanes
... [ATpoint][1] I am trying to understand the script, can you please comment so that I can understand it properly. Normally we pass single ended fastq files seperated by comma, but I didn't see anything after -U - , can you please also explain this thing? [1]: https://www.biostars.org/u/25721/ ...
written 9 days ago by waqaskhokhar99910
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Comment: C: Alignment of single-ended library distributed among different lanes
... [ATpoint ][1]the previous version of samtools was 1.7 but now i updated to latest version (1.9) but still getting this error: [E::hts_open_format] Failed to open file Alst-1_6989.bam samtools view: failed to open "Alst-1_6989.bam" for reading: No such file or directory Error: reads file ...
written 9 days ago by waqaskhokhar99910
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Comment: C: Alignment of single-ended library distributed among different lanes
... [ATpoint][1] I got this error now, does that mean we need to adjust .bam file in the code? [E::hts_open_format] Failed to open file Alst-1_6989.bam samtools view: failed to open "Alst-1_6989.bam" for reading: No such file or directory Error: reads file does not look like a FASTQ file ...
written 10 days ago by waqaskhokhar99910
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Comment: C: Alignment of single-ended library distributed among different lanes
... I have made a layout.txt as: data/1547_2015/Accessions/Alst-1_6989/transcriptome/fastq/trim/SRR3460433 Alst-1_6989 data/1547_2015/Accessions/Alst-1_6989/transcriptome/fastq/trim/SRR3460434 Alst-1_6989 data/1547_2015/Accessions/Alst-1_6989/transcriptome/fastq/trim/SRR3460435 Alst-1_69 ...
written 10 days ago by waqaskhokhar99910
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Alignment of single-ended library distributed among different lanes
... I want to perform alignment using **Hisat2** for single-ended thousands of samples and each sample distributed among different libraries. I have modified this script (https://www.biostars.org/p/223404/#224169): #!/bin/bash for f in `ls data/1547_2015/Accessions/Alst-1_6989/transcriptome/fa ...
alignment rna-seq written 10 days ago by waqaskhokhar99910
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Answer: A: Cut off for DE genes
... log2 fold change can give you better insight of the picture. For more details you can check these links [RNA-Seq workflow for differential gene expression][1] [From reads to genes to pathways: differential expression analysis of RNA-Seq experiments using Rsubread and the edgeR quasi-likelihood pip ...
written 4 months ago by waqaskhokhar99910
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Comment: C: Bowtie indexes for custom reference genome
... yes we don't need gtf file to build genome index. Good luck ...
written 4 months ago by waqaskhokhar99910
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Answer: A: Bowtie indexes for custom reference genome
... Bowtie can index from a set of DNA sequences. It produces six file which constitute the index. For more details please check this link [manual section on index building][1] [1]: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml#the-bowtie2-build-indexer ...
written 4 months ago by waqaskhokhar99910
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Comment: C: limitations of Edge R or DEseq
... In case you want to see DE among large number of samples and you don't have replicates you can use EdgeR. Please see the section 2.11 [What to do if you have no replicates][1] [1]: https://www.bioconductor.org/packages/release/bioc/vignettes/edgeR/inst/doc/edgeRUsersGuide.pdf ...
written 4 months ago by waqaskhokhar99910
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Answer: A: limitations of Edge R or DEseq
... DESeq is not suitable if you don't have biological replicates but EdgeR can calculate differential gene expression even you don't have biological replicates. ...
written 4 months ago by waqaskhokhar99910

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