User: 200dumplings

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200dumplings10
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Posts by 200dumplings

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ReactomePA only showing one pathway
... After I run the enrichPathway() on my genelist, I tried to visualize it using barplot(), but it is only showing one enrichment pathway. In my S4 results, I have definitely more than 1. I was wondering if anyone can help? My input data looks like this head(genelist,50) > [1] 14013 76589 ...
reactomepa reactome written 16 months ago by 200dumplings10
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Comment: C: MACS2- struct.error: unpack requires a string argument of length 4
... Also checked the control file, it turned out to be empty. I think maybe something happened when I was removing the blacklist regions? ...
written 16 months ago by 200dumplings10
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Comment: C: Bowtie2: Error: No input read files were valid
... Yes hahah I fixed it by giving it the actual directory. Thank you! ...
written 16 months ago by 200dumplings10
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Comment: C: MACS2- struct.error: unpack requires a string argument of length 4
... The output of `samtools quickcheck -qvvv input_Meis1_native_D02.bam` is: verbosity set to 3 checking input_Meis1_native_D02.bam opened input_Meis1_native_D02.bam input_Meis1_native_D02.bam is sequence data input_Meis1_native_D02.bam had no targets in header. input_Meis1_native_D02.bam cannot be chec ...
written 16 months ago by 200dumplings10
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MACS2- struct.error: unpack requires a string argument of length 4
... Command line: callpeak -t filtered_H3K9ME3_MEIS1_NATIVE_A10.bam -f BAM -c input_Meis1_native_D02.bam -g mm --broad --broad-cutoff 0.1 ARGUMENTS LIST: name = NA format = BAM ChIP-seq file = ['filtered_H3K9ME3_MEIS1_NATIVE_A10.bam'] control file = ['input_Meis1_native_D02. ...
macs2 chip-seq written 17 months ago by 200dumplings10 • updated 17 months ago by ATpoint39k
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Bowtie2: Error: No input read files were valid
... bowtie2 -x mm10 -q -1 /PX0315/C89CJANXX_2/PX0315_AACCCC/C89CJANXX_2_AACCCC_1.fastq -2 /PX0315/C89CJANXX_2/PX0315_AACCCC/C89CJANXX_2_AACCCC_2.fastq -S H3K4ME1_NATIVE_A03.sam > ERROR: > stat: Bad file descriptor > Warning: Could not open read file "/PX0315/C89CJANXX_2/PX0315_ ...
bowtie2 chip-seq written 17 months ago by 200dumplings10 • updated 17 months ago by h.mon31k

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