User: saadleeshehreen

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Posts by saadleeshehreen

<prev • 63 results • page 1 of 7 • next >
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How to write a proper bed file to extract sequence?
... Hi, I have manually created a bed file to extract the sequences from a fasta file. But it is showing the following error message. How can I solve it? -bash-4.2$ cat pAcr_extract.bed PSE305_1 20001 20479 PSE305_1 20306 20479 PSE305_1 20001 20303 AZPAE14907_contig_18_1 20001 204 ...
extract_seq bed file covertor written 1 day ago by saadleeshehreen40 • updated 1 day ago by mike-zx50
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Salmon error message
... I am trying to quantify the expression of my genes by using salmon. The command is following salmon quant -p 10 -i ensembl_index/ -l A -1 SRR1056045_2.fastq.gz -2 SRR1056045_1.fastq.gz -o ensembl_quant But got the following error message: Error reading from the FASTA/Q stream. Minimum r ...
salmon rna-seq written 5 days ago by saadleeshehreen40 • updated 5 days ago by Devon Ryan85k
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Comment: C: Problem to Understand the visualization of IGV
... Its my first time I am working with IGV , BWA and samtools. I tried the same procedure with other genome and didn't see such alignment there. That seems quite normal. I don't know what happens with it. What do you mean by 'read groups'? ...
written 7 days ago by saadleeshehreen40
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Comment: C: Problem to Understand the visualization of IGV
... red one ... ...
written 7 days ago by saadleeshehreen40
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Problem to Understand the visualization of IGV
... I use BWA to create a bam file and visualize the alignment with IGV. I didn't split the window. But I get two alignments exact at the position of my gene of interest. What does it mean? ...
dna sequence visualization igv written 7 days ago by saadleeshehreen40 • updated 7 days ago by Devon Ryan85k
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Comment: C: loaded a sorted bam file in IGV but I can't see anything
... Thanks. I use BWA and now the alignment look like that.. I didn't split the window. But I get two alignment near the position of my gene of interest. What does it mean? ...
written 7 days ago by saadleeshehreen40
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Comment: C: loaded a sorted bam file in IGV but I can't see anything
... Red box is the region I want to see. The file is quite different from the tutorial page. Shouldn't I saw grey bars for bam files? https://wikis.utexas.edu/display/bioiteam/Integrative+Genomics+Viewer+%28IGV%29+tutorial My intention was to understand the piece come from any integrated elements or no ...
written 8 days ago by saadleeshehreen40
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loaded a sorted bam file in IGV but I can't see anything
... Hi, I have genomic SRR file (DNA-seq) for a pseudomonas genome. I used a file containing corresponding cDNA sequence and nucleotide sequence of my gene of interest to build the index by using the salmon tool. Then, used samtools to create SRR.bam file salmon quant -p 10 -i SRR_index -l A -1 ...
assembly bam igv written 8 days ago by saadleeshehreen40 • updated 8 days ago by Emily_Ensembl16k
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Comment: C: What is the meaning of alignment strand plus/minus in blastn?
... Thanks. My GOI is in the integrated phage/plasmid ( not sure!), so in some genomes they are same orientation of upstream genes ( in those cases, the strands were plus/plus for both of the promoter and GOI). But whenever the upstream genes are in opposite orientation, the strands were plus/minus for ...
written 9 days ago by saadleeshehreen40
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What is the meaning of alignment strand plus/minus in blastn?
... Hi, I am intended to analyze the promoter sequence of my gene of interest (GOI). I extracted the promoter sequence (200 bp) by using a in-house tool. Some portion of the promoter (90 bp) came from upstream gene( it could be putative as no known annotation for the protein).The artemis view of .gbk ...
blastn written 9 days ago by saadleeshehreen40

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