User: fmerkal

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fmerkal10
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New User
Location:
USA/Lowell/University of Massachusetts Lowell
Twitter:
@merkuri_fm
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1 week, 2 days ago
Joined:
8 months, 1 week ago
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Posts by fmerkal

<prev • 10 results • page 1 of 1 • next >
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Interpreting liftOver output to extract orthologous exons between distantly related species.
... Hello everyone, I am trying to use RNAseq data to analyze differential exon usage between two distantly related species (mouse vs chick). The problem I have encountered has to do with extracting orthologous exons between mouse and chick. When comparing the splicing profiles between these two specie ...
genome R rna-seq written 7 months ago by fmerkal10
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Comment: C: Gene Set Clustering based on Functional annotation (GeneSCF)
... MacOS Mojave 10.14.2 ...
written 8 months ago by fmerkal10
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Comment: C: Gene Set Clustering based on Functional annotation (GeneSCF)
... Hello, I intend to use GeneSCF to perform enrichment analysis. I am trying to prepare the database (goa_chicken) prior to running the analysis but I get this message that reads `Extracting goa_chicken information... cat: /Users/fjodor/Desktop/geneSCF-master-source-v1.1-p2/class/lib/db/goa_chicken/ge ...
written 8 months ago by fmerkal10
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Comment: C: (edgeR-related) DGElist error message 'Negative counts not allowed'.
... Hi, I was thinking about summarizing over genes instead of exons, after reading your comment, but I am interested in looking at alternative splicing as well as differential gene expression so I think that wouldn't be a good idea for my situation. I looked more into this problem and found out that t ...
written 8 months ago by fmerkal10
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Comment: C: (edgeR-related) DGElist error message 'Negative counts not allowed'.
... Yes, I did remove the header and gave the counts columns easier names. Geneid Chr Start End Strand Length FL1 FL2 HL1 HL2 ENSGALG00000054818 1 9774 10061 - 288 0 0 0 0 ENSGALG00000054818 1 9314 9364 - 51 0 0 0 0 ENSGALG00000054818 1 8674 8904 - 231 2.10 1.67 1.33 2.20 ENSGAL ...
written 8 months ago by fmerkal10
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Comment: C: (edgeR-related) DGElist error message 'Negative counts not allowed'.
... Hello, Thank you for your reply! This is a great idea and I tried it. The only issue is that there appear to be non-unique values in the Geneid column and this doesn't allow me to set the Geneid column values as row names. Could I still keep the R assigned row names and only delete columns 2:6? ...
written 8 months ago by fmerkal10
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(edgeR-related) DGElist error message 'Negative counts not allowed'.
... Hello, After counting genomic features with `featureCounts` featureCounts -F GTF -t exon -g gene_id -f -O --minOverlap 2 -M --fraction -J -a annotation.gtf -o out.txt 1_sorted.bam 2_sorted.bam 3_sorted.bam 4_sorted.bam I decided to use the output file as an input for edgeR to create the DGEli ...
software error R rna-seq written 8 months ago by fmerkal10 • updated 8 months ago by Gordon Smyth1.1k
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Answer: C: SAM to BAM conversion problem after HISAT2.
... Hello, I think I might have solved the problem. I used `samtools sort` to sort the SAM file and output it to BAM format with the command `samtools sort -o out_sorted.bam out.sam`. This seems to have created a BAM file that has a reasonable size ~2.9 GB (relative to the SAM file) and that I can view ...
written 8 months ago by fmerkal10
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Comment: C: SAM to BAM conversion problem after HISAT2.
... Hi, I did not use `nohup`. I am running hisat2 on a cluster and I received an output describing the alignment rate (overall alignment ~92%). I did not see other files, like the various .log files you would get if you ran Tophat. The output I get with `head out.sam` is listed below. @HD VN:1 ...
written 8 months ago by fmerkal10
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SAM to BAM conversion problem after HISAT2.
... Hello, I recently used HISAT2 to align my paired-end reads to a reference genome. The command I used was `hisat2 -q -p 4 -x path_to_index -1 reads_1.fastq -2 reads_2.fastq -S out.sam`. This produced a SAM file that was ~14 GB and had headers that matched the ones I looked up online for this type ...
software error rna-seq written 8 months ago by fmerkal10 • updated 7 months ago by eennadi0

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Popular Question 4 months ago, created a question with more than 1,000 views. For (edgeR-related) DGElist error message 'Negative counts not allowed'.

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