I use mmseq package, and happen the follow problem
[leo@liu mmseq]$ head SR016359.1.exp.gene.mmseq
# Mapped reads (or read pairs): 6120659
gene_id log_mu_em log_mu_gibbs mcse weighted_length
ENSG00000000003 1.23277 1.22626 0.00597861 1784.14
ENSG00000000005 NA NA NA NA
ENSG00000000419 2.22127 2.11945 0.00583188 1040.51
ENSG00000000457 0.958256 0.837237 0.00850429 2854.55
ENSG00000000460 0.657037 0.615422 0.00951234 3696.15
ENSG00000000938 1.68165 1.59352 0.00655677 1745.39
ENSG00000000971 1.23488 1.23017 0.00478502 4283.87
ENSG00000001036 1.97813 1.8715 0.00458929 1654.84
[leo@liu mmseq]$ head SR016359.1.exp.mmseq
# Mapped reads (or read pairs): 6120659
transcript_id log_mu_em log_mu_gibbs mcse length
ENST00000539570 -inf -11.5734 0.33027 710
ENST00000576455 -0.890898 -6.78479 0.355641 2012
ENST00000510508 -180.836 -11.0123 0.322965 881
ENST00000474471 0.71319 -6.78531 0.40447 1175
ENST00000381700 NA NA NA 320
ENST00000445946 -1.1245 -1.5426 0.03394 503
ENST00000472572 -40.0731 -7.81427 0.39148 1052
ENST00000420022 0.828722 0.742549 0.0130477 428
what is meaning for "NA" in output file?
My command line:
bowtie -f -a -S -m 100 --fullref -p 2 /home/leo/BitSeq/Homo_sapiens.GRCh37.67.cdna.all \
/home/leo/cufflinks/MAQC.RawData/SRX016359.1.fasta | samtools view -F 0xC -bS - | samtools sort -n - SR016359.12.namesorted
bam2hits -m "(E\S+).*gene
E\S+).*" 1 2 Homo_sapiens.GRCh37.67.cdna.all.fa SR016359.12.namesorted.bam > SR016359.12.hits
mmseq SR016359.12.hits SR016359.1
[leo@liu mmseq]$ head SR016359.1.exp.gene.mmseq
# Mapped reads (or read pairs): 6120659
gene_id log_mu_em log_mu_gibbs mcse weighted_length
ENSG00000000003 1.23277 1.22626 0.00597861 1784.14
ENSG00000000005 NA NA NA NA
ENSG00000000419 2.22127 2.11945 0.00583188 1040.51
ENSG00000000457 0.958256 0.837237 0.00850429 2854.55
ENSG00000000460 0.657037 0.615422 0.00951234 3696.15
ENSG00000000938 1.68165 1.59352 0.00655677 1745.39
ENSG00000000971 1.23488 1.23017 0.00478502 4283.87
ENSG00000001036 1.97813 1.8715 0.00458929 1654.84
[leo@liu mmseq]$ head SR016359.1.exp.mmseq
# Mapped reads (or read pairs): 6120659
transcript_id log_mu_em log_mu_gibbs mcse length
ENST00000539570 -inf -11.5734 0.33027 710
ENST00000576455 -0.890898 -6.78479 0.355641 2012
ENST00000510508 -180.836 -11.0123 0.322965 881
ENST00000474471 0.71319 -6.78531 0.40447 1175
ENST00000381700 NA NA NA 320
ENST00000445946 -1.1245 -1.5426 0.03394 503
ENST00000472572 -40.0731 -7.81427 0.39148 1052
ENST00000420022 0.828722 0.742549 0.0130477 428
what is meaning for "NA" in output file?
My command line:
bowtie -f -a -S -m 100 --fullref -p 2 /home/leo/BitSeq/Homo_sapiens.GRCh37.67.cdna.all \
/home/leo/cufflinks/MAQC.RawData/SRX016359.1.fasta | samtools view -F 0xC -bS - | samtools sort -n - SR016359.12.namesorted
bam2hits -m "(E\S+).*gene
![Frown](https://www.seqanswers.com/core/images/smilies/frown.png)
mmseq SR016359.12.hits SR016359.1
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